If you watch her and listen to her words carefully, Saki actually wasn't that opposed to their actions and that upset Satoru further who then spent effort convincing her otherwise. That surprised me at first, I expected it to go the other way around. But then I remembered Saki never liked the fact that the queen once tried to kill Squealer.
So Saki was a bit horrified at the fact they had lobotomized her instead of some other method, but in truth she was having a difficult time finding faults in their logic.
What Saki didn't like was that Robber Fly was using the two of them as a shield and nuke. She recognized that right away, while Satoru didn't.
The pair are not as united as your post seems to imply.