I think the father stuff served as nothing more than just backstory. It was done, especially in the first one, to show that even though she was this beautiful, popular girl, she had issues at home, and that her life wasn't perfect.
I also mentioned this in a previous post, but MJ had daddy issues, and I think it was a way of explaining why she could never be alone, and why she always needed to have a man in her life to make her feel better. She quickly jumped to Harry after Flash broke up with her, and then she fell for Spider-Man who was always there to protect her. Then in SM2, even though it was obvious she was still in love with Peter, she was seeing John and got engaged to him, simply because he was there, and not because she truly loved him like she did Peter and Spider-Man. And in SM3, at the first signs of trouble with Peter, she was always looking for comfort from Harry.