They don't need to reboot the franchise. Not ever issue can be solved by scribbling out the last three movies. Hell, that's one of the things Superman Returns did right.
Honestly, the franchise, storylinewise is in a great place. Harry is dead, so there's no more of the Goblin crap. MJ and Peter are together, but in a rocky place. They can either bring them closer, via a supervillain getting their hands on her, or that could drive them apart, either by Peter saying that "It's too dangerous for you" or MJ actually dying. Fuck, they could even kill off Aunt May like Joey Q was too big of a pussy to do.