Bummer about the squirrel! I'll bet Pippin bit him in the neck or the back and damaged his spinal cord. If he doesn't recover but doesn't die, you might have to dispatch him yourself, or get ecurbh to do it. Not fun!
I think the squirrel is really shocky... I've been trying to leave him alone, but the last time I went out there he hadn't moved at all and was even less responsive. He'll die.... poor little guy.