Do you need another reason to be seen as a monster besides kidnapping seventy-five six year olds for the purpose of performing grisly medical procedures on them with a nearly 50% mortality rate? Cause uh, that's pretty monstrous. What about growing a bunch of flash clones of them that have full awareness and sentience, both to salve your conscience and to let their parents see them die so they wouldn't keep looking for their children? What about growing a clone of yourself, or your brain, at least, for the purpose of harvesting it to create an AI? What about abducting war assets that could have saved hundreds, if not thousands, of lives during the battle for Earth and taking them to a safe place to soothe your own conscience? I like the Halsey character. I think she's fascinating. I don't think she's an irredeemable person, but surely you can see why people on the other end of the stick do. If you don't, that's fine, I guess, but I'm not going to keep making an argument that's been done a thousand times about why people treat her the way they do.
Look, I'm not going to get into an "ends don't justify the means" argument, because I don't know exactly where I stand on that, especially in the context of the Halo universe and the situation they were in, but I like that the book finally puts that question at the forefront by presenting people on both sides of it, regardless of the entrenched fiction that's accepted it so far. This stuff happens all the time. Look at the Guantanamo situation.
And yes, destabilizing a former military superpower when they're down makes a lot of sense, especially if you find yourself in a winning position all of a sudden and your relationship with them is tenuous at best. It's ONI's job to cement that victory by slowing down the Elites' recovery from the Schism, because once Infinity's ready to go, it doesn't seem like anything they've got is gonna be able to stop it.