You can't use instances if you intend to turn them all to separate rigid bodies afterwards so you'd have to duplicate instead. Nevertheless it sounds like you're trying to do something overly heavy with rigid bodies. I would probably create few rigid body hero bits manually and think of using the particle geometry instancer for the rest. Then again I still don't know what your scene is all about

I have actually done something like this before. I had a particle flow system which was moving soft-body driven geometry (blood cells in a vein). The softies were created and maintained (and removed) on the fly in the particle's creation/runtime expressions. It worked but I remember it being a very "hairy" setup