What gets forgotten about is that Peter and MJ aren't even a unique case, they just happen to be the one pairing you thought would always be above a persistent problem at the company, and that is that Happy endearing relationships are something you rarely find in any Marvel title.
To demonstrate how absurd this can get, take Mss. Marvel, still a fairly young title, which had the popular will they/won't they pairing of Bruno and Kamala, and that was in it's infancy when it was derailed by Civil War II...they're teasing it again now (albeit as part of a triangle) but there was a phase the two were not on good terms and it upset the fans.