Hi,
I would definately keep him in his own enclosure for feeding if that is what has worked best.
The cage aggression thing really isn't all that common a problem with ball pythons - they tend to be more nervous than agressive. In the case of the really nervous ones moving them to a container can positively ensure they won't eat.
I am kind of dissapointed in the shop for selling you a snake they hadn't got to eat and were forcefeeding - it speaks volumes about them in fact.
How big is your snake - it may be he could handle slightly larger prey.
But remember the most important thing is to let him settle in and avoid handling for a week if possible - and definately none for the next 48 hours to give him a chance to digest his dinner.
Have a read of the caresheet on the site to see if it gives you any questions you'd like to ask.
dr del