Malcolm, who respects the system that is in place, understands that his inmate boyfriend needs a Warden because that's Will's ticket off this ship, someone to help him. You two don't have to get along for Will to graduate or for them to have a relationship - I never got on particularly well with Jedao when I was married to his. [Raylan had his own theories on that, but that kind of mess didn't belong in this conversation.]

Malcolm's a Warden too, and he's graduated one soul already. He's your ally in every single one of the goals you mentioned; it's all in his interests.