I am familiar with the Faraday Effect, but I remain confused as to why the electric and/or magnetic components of light do not naturally align themselves with a magnetic or electric field (in a vacuum) and thereby become polarized.
The Faraday effect is dispersive, so it is coherent and reversible. It tweaks the evolution of the light but doesn't cause "relaxation". In general, a system cannot reach a ground state, like becoming aligned to a magnetic field, without some sort of dissipation (e.g., absorption).
The linear algebra way to think about this is as follows: consider orthogonal states of light, such as $H$ and $V$ linear polarizations. After coherent evolution, they remain orthogonal, or else the evolution would not be reversible (given the final state, the initial state can be uniquely determined). This logic shows us the range of possible options for coherent evolution. The polarization can rotate (like the Faraday effect), it can go from linear to elliptical or circular (like a quarter waveplate), or it can undergo a mirror reflection (like a half waveplate). Of course, any combination of those options is also valid. But it can't align without ''losing information'', which would require a absorptive polarizer. (What I've just described is the $U(2)$ group of unitary matrices on $2\times 2$ complex vectors.)
Note: when I say "reversible", I mean coherent or unitary. I'm not referring to time reversal symmetry, which the Faraday effect breaks.
Edit If we're looking for a way for light to align to the magnetic field, we need the information on the original polarization of the light to be lost. The Faraday effect is off-resonant and cannot achieve that. One way to realize this is through dichroism, where one polarization (usually circular) of light is absorbed. This process is clearly not coherent/unitary because it erases the information on what the incoming polarization is. After absorption, with the right setup, the light can become aligned with the magnetic field. (I can give an explicit example with atoms, if you'd like.)
Sorry if this repeats my comment.
Light does become polarized in the presence of a magnetic field. That is how some 3-dimensional maps of the magnetic field lines above certain surface structures of the Sun are recovered, by means of observing the direction of polarization of light of a specific infra-red line, that arrives from the photosphere. I remember it was a paper in Nature by Krupp and Collados and others. It is a relatively recent technique (from the last decade, I think) because it was technically difficult to observe the polarization of light from the Sun until recently.
I think the crux of the matter lies in your :
why the electric and/or magnetic components of light do not naturally align themselves
What does "align" mean other than an interaction?
So the question "do photons interact with an electric or magnetic field in vacuum"? has to be answered first before going into the details of the type of interaction.
The answer to this last is "yes, with very very small probability". It is called Delbruck scattering and has been experimentally observed.
It is a QED only effect, it does not exist in classical electromagnetic theory and the measurements are used as an experimental confirmation of QED. It is evidence of vacuum polarization in the strong electric fields of nuclei.
So the photons do interact with the fields through higher order QED diagrams, and not simple higher order, the lowest order allowed is sixth order, which makes this interaction very improbable. It is small in the strong fields around nuclei, it is infinitesimal in the distant coherent fields of atoms, which is what an electric or magnetic field is in vacuum. To have any fields you need the electric and magnetic sources of atoms.
The "infinitesimally low probability of interaction" is what negates the "natural" in your question. A beam of photons does not align its electric or magnetic field to the direction of electric and magnetic fields in vacuum because the interaction probability is practically non existent.
@QuantumDot You seem to be close to the answer to this question. Neither the electromagnetic field Lagrangian nor the gauge theories of fundamental interactions include interactions between photons and electric or magnetic fields. An electric or magnetic field, on their own, represent very low energy photons. To say that a photon interacts with a magnetic or an electric field would suggest that photons interact among themselves. Photon-photon interactions are possible via two fermion 'square' loops, like e- e+ for example. Furthermore photons have neither electric nor magnetic dipole moment. Hence your suggestion that photons pass through an electric or magnetic field undisturbed is right. I have increased your comment by 1.
I think, from a viewpoint of photonics, light, or photon, can only interact through charge and gravity. View light as bosonic vibration of space-time. Charge is the source for such vibrations and responsible for scattering, absorption as well. Gravity affect light because gravity is the curvature of space-time itself.
From a pure wave picture, any effect of light is tracked down to the effect of wave-interference: The scattering is the wave generated by dipoles inside matter excited by incident wave; absorption is simply the scattered wave out of phase with respect to incident one, nonlinearity is anharmonic scattering, etc, etc. Wave themselves simply add up by principle of interference without changing each other's internal property. Polarization is such a property. Hence light add up with another light will not change either's polarization, although they may form a standing wave or beat.
Light does become polarized in a magnetic field. The magnetic field of a black hole was detected due to the polarization of light. Check this article: http://www.iflscience.com/space/black-holes-powerful-magnetic-field-observed-first-time