If one of my opponent's Pokemon is Knocked Out in the middle of a turn before the attack, can I take my prize(s) right away or do I have to wait until the end of the turn?
No matter when a Pokemon gets Knocked Out during a turn, the opponent takes their prize(s) as soon as all triggered effects have finished resolving. You do not wait until the end of the turn to resolve KO's and prizes.
Source: TPCi Rules Team (2018-04-05)