On one hand, allowing Bass to remain a threat could be considered wrong. But wouldn't changing him from what he is also be wrong? The point is moot really, since Bass isn't going to give him the option.
Couldn't Bass just go anti-hero and hang out with Proto Man? He doesn't let Dr. Light repair him either, and does all his own repairs. I'm pretty sure that, as long as Bass promised not to perform acts of senseless violence, and just do battle with Mega Man every so often, Proto Man would be willing to help with his repairs. Proto Man would probably see Bass' constant battles with Mega Man the same way he viewed the times he attacked Mega man during the games - forcing Mega Man to constantly improve.