Look at the Space Jockey in Alien for example. Many Sci-Fi franchises have a mysterious faction in their backstory that just serve to flesh out the universe. The forerunners were defeated to serve as a writing tool to make the flood seem very powerful, they dont serve much purpose other than that. No way to find them all or be sure they're all gone. The only sad thing is if humanity survived and spent the next thousand years exterminating markers, it will only take one survivor to restart everything and that survivor could have been around floating through space two million years or more relative to the events that occured to the alien civilization on Tau volantis. And by that point if humanity is smart enough they'll take time to properly decimate any marker they run into afterwards. But ships armed with planet cracking equipment could tear a moon apart in minutes.

Even nukes wouldn't do shit to these guys.

It was straight Lucky Isaac and Carver managed to conveniently have that amped kinesis pad and thousands of floating markers around to throw at the moon but any other human or group of humans with ships or not has no chance against them. That would probably be the best way to propose killing the moons.

Brethren moon dead space wiki