I still like my idea: Mata Nui reenters his body, Makuta is forced out of the body in his infected Tohunga/Matoran form, which falls and burns up in the atmosphere.
It's epic, it's fitting, Mats gets his body back, and it references 2001.
Only problem is that it doesn't give him a way of still being alive like we all know he is.
I don't like the idea of a sudden change of heart, though. If that was going to happen, it should be because Makuta is trying to save his own skin and/or inadvertently helps Mata Nui fix stuff then is hit by a rock or what I mentioned above.
Also the "Makuta = puppet" theory would basically destroy the entire BIONICLE story's base. Up until now, Makuta's been the big über-badguy who's orchestrated every nasty thing that's happened. For him to suddenly be just another pawn would be a bit too much.