With the identity getting techno-magic-science wiped from the minds of everyone, Peter made the last second decision to not let MJ lose her memories along with everyone else because he needed her. MJ doesn’t see this as him doing it to save their relationship and lives, no, she doesn’t see it as going back to a status quo that existed for decades. She sees it as him being selfish, and now she can’t deal with him anymore. Him not letting her get mindwiped with everyone else is the breaking point.
Not the mindwipe. The fact that she did NOT get mindwiped.