If you don't have a sealed battery cleaning can definately kill it if done impoperly, it all depends how they cleaned it and what they cleaned it with. Usually to get the corrosion and acid off you wash it with some kind of neutralizing agent (at home I use baking soda and water). If the mixture gets past the caps it can neutralize the acid that you want to keep (in the battery).

They'd have to be pretty sloppy to completely kill a battery but if it was already half dead it wouldn't take much more to finish it off. Having the battery die right after they cleaned it isn't a coincidence, tell them you want the cost of the stock battery credited to you and use the money to help buy an Optima sealed battery.