The notion of the continuum in physics is not as a collection of differentiated points gathered together into an abstract set, but as a limit of discrete structures with finite computations defined on them. The limiting process must be well defined, so that the answer to any experimental question to any accuracy can be answered by a finite computation.
Any set-theoretic property of the collection of the real numbers which relies on separating out individual points from one another in a non-computable way and talking about them using logical properties of the individual points which involve undecidable questions is always going to be unphysical. This is true for much milder collections than those involved in Banach-Tarsky style constructions.
For example, consider the collection of all real numbers whose digits encode the solution of the Halting problem (the collection of all Turing degrees above 0'). There is a logical predicate which will describe these numbers--- there exists a computer program which takes the digits of this real number, takes a computer program, and spits out the answer to the question "Does the program halt?" after a finite number of steps. So this collection of numbers is well defined as a logical construction (at least in an ordinary set theory). This is a predicatively defined collection of real numbers, which makes sense as a set in mathematics.
But is it meaningful to formulate a theory where the electron behaves differently when it is located at one of these special points? Obviously not! The behavior of the electron in a physical theory must be described by a finite computation, not by an abstract logical game over all the digits of its position. The fundamental principle in physics is that computation is fundamental, not set theory. The idea that physics is computable is the foundation of the science--- physics looks for a computer program which matches the behavior of physical objects. It does not look for an axiomatic set theoretic structure which matches the behavior of these objects.
This principle has been sometimes challenged, but the challenges are mostly silly. It is not directly relevant to your question, because you are interested in Banach-Tarski.
The analogy of Banach Tarski with the Turing degree undecidability is actually awful, because the Banach Tarski paradox is of a far more non-constructive nature, in that it is not even possible to define reasonable properties of points which are in one or the other of these Banach Tarski sets. You can't find a predicate for separating out the points of these sets, even using super-duper-duper computation of any strength. Defining Banach Tarsky sets relies on a notion which is worse than computationally undecidable, they rely on a predicatively undefinable notion. You can't decide whether the points fall into this or that uncountable choice collection using any sort of predicate which does not refer to a choice function.
The only good analogy is not much of an analogy at all, the Banach Tarsky business is just identical in philosophical annoyance to every other axiom of choice construction where you apply the axiom of choice to a set of size continuum or higher. The countable axiom of choice is not a problem, nor is the axiom of choice on any uncountable sets you care to introduce which are not as big as the continuum. But the moment you can do uncountable choice on the continuum, you get paradoxes with probability.
The basic reason is that the notion of probability is intuitively well defined--- you can pick a real number at random by flipping coins at each step to pick the binary digits. But once the random real number is calculated to infinite precision, you can then ask "does it belong to this set S or not?" For every set S. This means that every subset of [0,1] has a notion of measure, which is the probability of a random number landing in that set.
This idea is the basic conflict between the axiom of continuum choice and the theory of probability. If you allow yourself to choose continuum many points, you can construct sets which are not measurable. If you do not allow yourself to do this, you can make every subset of [0,1] measurable. Whether you decide to have choice or probability is up to you, and most mathematicians choose choice over probability. This is stupid, and it makes measure theory difficult because you have to restrict yourself to measurable sets, and these measurable sets include every set you can ever imagine, including all the Turing degree shenanigans, and even higher undecidable stuff, excluding only impredicatively defined selections using continuum choice.
So I consider Banach Tarsky type results to be far worse than unphysical, they go so far as to be non-mathematical--- they should be considered false even as pure mathematics. This is to be distinguished from the concept of the real number whose digits encode the solution to the halting problem, which you can pretend exists in a real sense without any damage (although you still need to be careful to note its non-computable nature). There is no benefit whatsoever to including choice constructions on the real numbers, and there is much harm to the theory of integration and probability.
Computation in mathematics
Even within pure mathematics, the mechanism of logical deduction is always a finite computation. If you are given a well defined collection of axioms, or axiom schemas all of whose axioms can be listed by a computer program (this includes every reasonable mathematical theory), you can write a computer program to deduce all the consequences of these axioms. Godel's completeness theorem states that every deduction will be reached by the rules of first order logic, and that when there is an undecidable statement, one which cannot be proved or disproved by the axioms, there is always a model of the axioms where the statement is true, and a model where the statement is false.
This means that when you are given a set theory, which talks about infinite non-denumerable collections, you can understand that the theory is really talking about its countable models, and this gives a countable computational interpretation to every theorem. You can then ignore the jibber-jabber about the theory talking about some enormous sets, and consider the theory as talking about its countable models.
So, for example, when a theory is saying "all real number can be matched one-to-one to aleph-1", you can understand this to mean "all the countably many real numbers in any countable model of this theory can be matched 1-1 to the countably many elements of aleph-1 in this theory using a function symbol which is defined within the theory". You also know that "R is uncountable", meaning "for any function symbol in the model of the theory, mapping the integers to R, there exists a real number x which is not in the range of this function symbol." This does not make the real numbers in the model uncountable, of course, it is only saying that the theory is strong enough to prove the uncountability of R, so it can never identify the countability of the reals in any of its models from within.
Then mathematical theories never talk about non-denumerable infinities, except as a very useful figure of speech, and all questions about whether a theorem is provable or unprovable are equivalent to questions about countable structures whose properties are generated by an explicit computer program.
It is important to always have this point of view in the back of the mind, because it makes the undecidability results of set theories completely intuitive. If you think of the sets in set theory in Platonic terms, it is very difficult to make sense of the undecidability results, nor of large cardinals, or of anything else.
How Does Banach Tarski work?
In order to explain Banach Tarski, it is best to consider simpler constructions which predates it by half a century. The first such "theorem" is the well-orderability of R. This is done as follows:
consider the set S of all nonempty subsets of R. Choose an element from each member of S, that is, for every nonempty subset of R, pick one element. Now consider R. This is a nonempty subset of R, so you picked some element. Let this element be x(0). Now consider R-{x(0)} (the set R with x(0) omitted). You picked an element of this set, so call this x(1). Now consider R minus both x(0) and x(1). This is a nonempty subset of R, so you picked an element of this set, so call that x(2). Continue by induction to produce x(n) for all integer n.
Now continue the induction over ordinals. The first element you find past all the integers is $x(\omega)$, which is the element you chose from the set $R - \{x(n)|n\in Z\}$. Continue over every ordinal. It is easy to see that if you are ever get stuck in this inductive process, the reason must be that you have already listed every element of R, and this means that you have matched R to an ordinal.
The remainder of the proof is to show that there must be a large enough ordinal to make this process end. The reason is that if there weren't, then this process would bound all the ordinals from above, allowing you to bound the collection of all ordinals using a set, but you can't, because if there is a set of all ordinals, it is an ordinal, and you could define this ordinal plus 1 for a contradiction.
This proof, if looked inside a countable model, is producing a matching between the countably many elements of R, and some countable ordinal in the model. This matching is simply a fake--- it is revealing that both R and the uncountable ordinal it is matched to are countable in the countable model.
So now to Vitali--- to make a Vitali set, you consider an equivalence relation on the elements of [0,1) (considered as the unit circle, so that addition and multiplication are modulo 1), so that x and y are equivalent if their difference is rational (this is completely predicative). Then you magically choose one element from each equivalence class, and gather these into a set S. This set has the property that countably many translates cover [0,1), so this set cannot have measure.
This is a silly construction, because any attempt to specify which points belong to S requires an inductive listing of all these points. This is tantamount to an ordinal description of R. So you have a set which is basically a long ordinal list of real numbers, one for each equivalence class.
Banach Tarski does the same thing, except using translations and rotations. In order to make a finite number of sets cover the two spheres, it is essential to use non-commutative rotations. The argument is much more complicated, but the philosophical difficulty is the same as always--- the notion of choosing a real number at random is conflicting with the notion of choosing continuum many elements of sets simultaneously.
Forcing
The way to say this precisely was found by Paul Cohen. The method of forcing allows you to add elements to R in a countable model in such a way that they can match one-to-one with an ordinal which is bigger than any ordinal you like.
The basic idea is to choose a real number at random for each of the countably many elements of the ordinal you want to fit into R. This is not precise, because the notion of randomness is too complicated, so Cohen used a purely logical notion of choosing a "generic" real number, which is defined by the process which decides which properties are true of this number. The procedure is described from a nearly completely computational point of view in Cohen's "Set theory and the Continuum Hypothesis", and it is not described from a computational point of view hardly anywhere else.
From similar constructions (but this time using probability), Solovay proved that it is consistent to allow all subsets of reals to be measurable. The consistency of set theory plus dependent choice (strong countable choice) plus Lebesgue measurability of all subsets of R is one of the most striking results of set theory--- it guarantees that there is absolutely no Banach Tarski style paradoxes for sets constructed in the usual way, using predicative definitions.
In other words, if you do not allow functions which select continuum many elements at once, Banach-Tarski fails. There is absolutely no mathematical theorem which depends on uncountable choice which is of use to mathematicians, and it is well past the time to scrap this nonsense.