Peter wasn't interested in her until he met her. It wasn't that he fell in love with her looks he fell in love with HER. Just because she happened to be gorgeous doesn't make him shallow.
Lol. Yeah I'm sure that's what every guy says who's dating a sexy supermodel. He fell in love with her brain
I've never understood the idea that admiring a woman's mind and admiring her looks are some sort of zero-sum competition where one negates the other. I've been privileged to know several women who were both stunningly beautiful and strikingly intelligent and kind. Their exteriors only complemented their inner beauty rather than competing with it.
Conversely, there have been a few women I've known who were utterly stunning to look at but had unpleasant personalities, and although I admired the view, I never came anywhere close to falling in love with them.
So I have no trouble believing that Peter fell for MJ for her personality rather than her looks. Especially since we literally saw that on the page. At first, Peter was attracted to MJ but only loved Gwen, and found MJ too flighty and shallow to be really worth his while. But after Gwen died, MJ revealed unexpected depth and kindness when she stayed to comfort him, and it was that emotional connection that was the real beginning of their relationship.