Psh, they don't get wiped out. I don't know what you're talking about. Destroy ends the cycle once and for all, life in the galaxy is free to evolve in the manner evolution actually works, and everyone lives happily ever after without being forced to look like green glowy freaks.
Exactly. GEE, THE LEADER OF THE MACHINES I HAVE BEEN FIGHTING FOR THE LAST 3 GAMES TRIES TO CONVINCE ME THAT KILLING HIM AND ALL HIS GOONS WON'T SOLVE MY PROBLEM EVEN WHEN THEY'RE THE DIRECT CAUSE OF THE CYCLE. Yeah, I'm sure that has a frigging ton of merit to it.
They're all bile space magic-fueled silliness, but Destroy is the least horrendous of the lot and the only one that actually accomplishes your goal.