It can be very simple.  A pool is penalized at the point it is caught - the earliest block where evidence is submitted.  There are 2 possibilities at that point.  1) The pool is still live - the owner's stake is destroyed and the pool is disbanded in this case.  2) The pool is old and does not exist anymore - simply do nothing in this case.  No harm can be done unless the attacking branch (can be long range attack) can get more signatures than the main chain.  The point is that if we can catch and penalize double-voting at the present moment, changing the history later is hard, unless an attacker can compromise most private keys of the pools.