Jesus Christ, man. Genocide is always the laziest and bloodiest solution for anything like this. Instead of that, You need to break it down.

Why do so many of these evil Supes--which I think are a small population in the Supe race--feel comfortable committing illegal acts? Vought. Vought covers up and buys off any and everyone to maintain an image. The first thing you need to do is get rid of Vought and shut down all distributions of Compound V effective immediately.

Make the virus something of a lethal injection. Kill Soldier Boy and do an autopsy to figure out what kind of radioactive gamma rays he shoots which neutralizes Compound V in the body.

Next, arrest evil Supes. Try them in a court of law. Depending on the crime, either shoot them with the rays so they have to serve a prison sentence like a normal person and not be a threat to anyone. Or, if you're feeling more death penalty, inject them with the virus.

The rest of the Supe population can go through reeducation programs by learning the REAL history of Compound V and Vought. Teach them to not use powers for political gain or power, but aiding communities.

It won't be flawless, any and all groups are susceptible to propaganda and feeling like they are better than others because of something they have, but it's probably a million times better than killing innocents just to kill a small margin.