You have to remember that at that point in time, Marvel were just beginning to recover after royally screwing themselves over in the 90's. So Fox and Sony were their best bets and they wanted to capitalize on their films as much as possible by tying the books to them (also why Mary Jane was hurriedly brought back to the Parker household as the romance was the crux of the Raimi films).
Personally, I feel the movie-inspired developments were for the better for both mutant and Spidey books. Like, who cared how they affected the Avengers lol. Just focus on your bread and butter. I know what Quesada was thinking with both HoM and OMD, but they definitely left their respective franchises worse for wear, not better. Incredibly telling that both X-Men and Spider-Man are reverting closer to their early-00's status quo.