I always got the feel that something like this was gonna happen with Hershel turning out to be some religious nut. Guess he has some sort of "edict" that any Walkers that they come across they save because eventually there will be a cure. Which is why Maggie looked horrified when they killed the one from the well.
I don't think it is a trap. More like a "Oh shit, they broke out! Who woulda thunk?! Welp, we're all dead!"