As in a word that means that the theory is too changed after all the accounting-for-criticisms, that its not really the original theory at all, and there's really not much more point in going on defending it?

I know this doesn't work much but you could try putting a few terms in here:
http://www.onelook.com/reverse-dictionary.shtml
its a reverse dictionary. I'll try first...
Hm... is it "obsolete"?
Outmoded, redundant, Superannuated.
That's the best I could get.