He's not sure if that would be better or much worse. The longer you stay here, the more you forget, after all. It's a choice between letting him go free to kill and die and letting him stay here to have pieces of himself chipped away.

"I'm not saying this is a good idea, but...what would happen if he stayed?"

From where he's standing, it looks like a choice between two deaths. Jay's not sure he's talking about Alex Kralie anymore.