That explains a lot.
Since it was determined the Rogue/Ninja was being dominated, he was not a traitor, anymore than if a giant had drugged him and used him to club your leader. In any fantasy realm where magic is commonplace, he'd be judged not guilty by reason of possession. And I assume your leader knew he was possessed.
And simply asking why an innocent person is being arrested is not a punch-worthy offense in any scenario I can think of. In fact, standing idly by is cowardice and a non-good sin of omission. (Using your leader's logic: you're in a dungeon, meet the boss who commands you to surrender. Clearly he must bow to the "authority" in the domain you've trespassed upon?)
So IMO you have much bigger problems. Your first, in my opinion, is that your current leader is a bully and a murderer, pure and simple. And if everyone else in the group is okay with his behavior, then that's your second problem.
A third is that your DM put your group in a series of situation that appear designed not just challenge, but to torment at least half of your party.
So whatever you decide you should do as a character, I know what I'd decide as a player: find another group. I found myself in a very similar situation when I learned the group and I had different ideas of what was "fun" and appropriate. I was so relieved and happy the night I told them I was gone. But maybe you have a higher tolerance for pain and frustration than I do.
(edit) In short, I think the answer to your original question is "five pounds of flax."
"Ceci n'est pas une pipe" - Magritte