Its a story. Characters are supposed to make a mixture of good and bad choices. The MC is a sixteen-year-old kid that is experiencing what its like to live in what was previously just a fictional universe. Do I really have to keep going?
He's only touching things that end up in his inventory. Also, if he does touch something that he doesn't put in there, he can just use his sleeve or something for like a door handle or whatever else.
While I can see how you may have come to the conclusion you did, I do not think, at least when I look back on it, that I made it come across that way. Those things don't always have to necessarily allude to something like that. I also don't remember specifically stating that he abused her with his pheromone manipulation, but that it was the power he received due to the fact that he is a mutant.