PAMELA is a particle accelerator which have two concentric rings, protons are accelerated in the inside ring. At ISIS muons are produced when a 800 MeV proton beam collides with a graphite target(carbon 12) can the same be done with this device? The accelerated protons from inside may be sent to the outside ring which will have slow carbon atoms and the collision will produce pions which will decay into muons. Do pions have any magnetic properties which can help to contain them after production?.
Pamela seems to have up to 250 MeV protons (I guess that's momentum) and up to 400 MeV per nucleon for the Carbon ions.
A carbon target has typically a higher density than a carbon beam (depending on how well the beam is focused however), so while one gets a higher center of mass energy in case of a carbon beam I claim that the collision rates would be much lower than for the target.
Wikipedia says that the ISIS neutron source is driven by a 160 kW proton beam (not the entire beam is used for muon production though). I doubt that a medical accelerator such as Pamela will have as much beam power or proton current. After all, beams in medical accelerators are shot onto patients...
charged pions are charged as their name implies and thus can be bent and focused like any other charged particle in dipole and quadrupole magnets. However, they have a lifetime of 26 nanoseconds which makes 'containment' very difficult...
From the tagging I suspect that you are thinking about muon catalyzed fusion. That poses some challenges beyond the ones you ask about, and I'll try to address those as well.
In other words, the proposed projects is very hard, would need to make a lot of fusion to pay, and almost certainly requires a built-to-order facility rather than trying to force a machine carefully engineered for other purposes to do the work.