I am aware of several angry letters written about Samus being a woman. But I did some digging and I think you are closer to right than I was. It seems that the average reaction was confusion. Like, someone (likely a boy named Justin Bailey) discovered a cheat code that, according to several publications such as Boy's Life, "turns Samus from a robot cyborg into a woman". It seems people just didn't know what to make of Samus taking off their suit and suddenly turning into a blond woman in a leotard. Based on my googling, it seems like many people were still confused about this when Metroid 2 came out in 91, but by the time Super Metroid came out in 94 most people understood that Samus was a woman the whole time.