I don't know what Bendis' feelings about MJ as love interest for Peter were. When he wrote her in Iron Man it didn't look as if there was much prospect of her being Peter's love interest in the medium future. He's definitely writing angsty MJ rather than party girl MJ, but he is writing her as a character and not just someone for Tony and Peter to fight over. (Looks sideways at Dan Slott.)
But having written MJ into Iron Man's comic, Bendis then didn't know what to do with her. Maybe some of that was Civil War II upending his plans. But anyway all the evidence is that Mary Jane works better when she's with Peter even with a sympathetic writer.