I'm definitely biased against him, because I was one of the players you mentioned. The thing is that even when you stop him, you know that the alternative is him raping her. If I remember correctly in one path he tells her to go to the bedroom before you stop him and get beaten up, so I don't think he just wanted to check if she made her bed in the morning... Also in one path you get the "she's horny because he used his powers on her and didn't fuck her" speech from Zel, while in the other one she doesn't appear horny at all, after the MC recovers from the beating.
I get what you're saying, but I think that since the NTR paths are possible outcomes depending on your choices, they are still canon, because everything else about him is exactly the same. For instance you can still get the implied NTR scene if he thinks that you're weak, no matter what you've done up until this point, so the paths aren't really that separated.
I know you didn't create this character and you're not responsible for his "introduction", but trying to make him likeable after that... Well, let's just say that I don't envy you for this task. Anyway, as long as we are not forced (and that's the key word here) to become buddies with him, there's no harm in trying. I guess it's a good challenge for a writer.