He doesn't want to erase their traits to erase their existence. He wants to erase their traits to end their sufferings. He's an omega as well. He knows the pain of being powerless to one's instinct. He's problem was that he made an assumption that ALL omegas feel like him when there are in fact a lot of omegas who are proud of who they are because they've learned to live with their omega trait and not fight it.
This dude, I think, is afraid of things like going into heat, getting raped, and maybe even get pregnant.
So, he's not a bad guy per his intentions, but how he goes about it does make him a bad guy.
What?! So that researcher is a bad guy?! Does he know our ML??! Get your hands away from herrrr!!!!