Or how about this: MJ's the one who gets shot rather than May. She pulls through, but Peter becomes convinced it's too dangerous for her to be around him, so he breaks up with her for her own protection. Or maybe he talks Dr. Strange into erasing everyone's memories of the marriage as well as his identity exposure, so that MJ and May will be safe and so he won't have to live with the pain of losing her. There are many ways they could've played it that would've made more sense than what they did.