Obviously it's temporary, what I mean is this: the switcheroo is that villain is now posing as the hero, so the hero is trying to prove to his friends they've switched bodies, ultimately does and switches back. That's the form and its fine. Now, you may have twists, turns and departures from that form (like the hero never getting back) BUT the point is the hero is trying to get back his life.
Now, another thing you can do that's part of the fun of the switcheroo is that the audience starts to empathise with the villain. This isn't required, but can be a lot of fun, as it is in FACE/OFF.
But whether the hero gets his body back or the villain becomes empathetic, the whole *spine* of the story is "the hero tries to get back his body".
If you *kill* the hero as soon as they switch bodies, who's driving the story? Well, it has to fall to one of the hero's sidekicks, but who? This is Spider-Man, not "Black Cat", and so who drives the story?
It's a self-defeating premise. Killing Spidey doesn't work because without Spidey, no one is driving the story. Even if you trapped Spidey in a prison for 12-issues, you could have him trying to break out (imspiderman.com) and then if he does, he's a fugitive and on and on, all the while Doc Ock has his own solo book or takes over the main book and is front & center, but Spidey has to be there or there's no story.
EDIT: Apparently, Spidey is in the afterlife fighting to get back, which would be akin to a prison except it still doesn't work; the *threat* of the story, what's at stake is Spidey's life. If he's in the afterlife with his family and friends and comes back to life, there is no jeopardy. Even if you have Doc Ock kill MJ, so what? *Shes in heaven now*. Even if Slott can somehow rectify these basic structural problems, these would only be solutions to problems that should never have existed.
Slott's better than this.