If he's used to taking f/t, he may have expended more energy in killing his prey (or, at least, trying to) than he would in just swallowing something that's already dead. Or, it's possible he wanted to start digesting immediately. Who knows what a snake thinks? It's all instinctual to them...

I have a milksnake that doesn't kill live prey... he just immediately begins swallowing it. You can see it moving inside of him after he's swallowed it for a bit, but he's never been hurt by it (he does this because he, too, is used to f/t).

It's happened to one of my BPs, too. Freaked me out the first time. But she was perfectly fine---in fact, the little bugger refuses to take anything BUT live now.