Maybe, but if you look at it that way Peter, and every other superhero, is destined to live and die alone unless they date within the superhero circle. If an extraordinary women like MJ (and past writers have written her as extraordinary) cannot come to terms and deal with her husband's double life then I doubt any woman plausibly can. It's especially annoying as Mary Jane was FINALLY getting the support system she needed by moving in with the rest of the Avengers. She needs someone to talk to? Why, there's Jessica Jones! Jarvis! Aunt friggen May! She no longer had to go out it alone, she likely should have been stronger in her resolve. Yet she crumbled, despite past writers having written her as coming to terms with Peter's night job. Of course that support crumbled with Civil War, and massive character regression and retcons, but still, it strikes me as a weak justification for the break up.