Its like Mark Hamill said, in SW Luke's lightsaber can cut Captain Americas shield into chunks, in Marvel Captain American's shield stops the light saber. If the PPG go to MHA, they fall under MHA rules and OFA can steal super powers.
That is a bit more debatable. OM was setting up Earth for an invasion, so he needed to take out all the people who could stop an invasion. OM likely misread Atom Eve's willingness/ability to protect the Earth, plus... other reasons. The Guardians had access to massive amounts of hardware, resources, and the ability to gather the planet together to fight the invasion, she did not.
What I'm getting at is Atom Eve was not enough of a threat to OM by herself that she would have presented a credible threat to the invasion force, plus he probably felt like she could be brought in line. The PPG are incorruptible, they would absolutely have resisted and were strong enough to pose a threat. That's a killable combination.