As I see it, Rodney has made his decision a few hours ago when he decided to not oppose Weir and Sheppard's decision to order Kavanagh tortured. I believe he is glad to have earned back enough of Weir and Sheppard's trust to no longer feel outcast after his actions in "Trinity" and was unwilling to rock the boat and risk it all again for a man he doesn't even like. Which makes it all the more tragic in my eyes - Kavanagh is one of his people, and thus deserving of his protection.
Rodney's failure in that respect is at least as tragic as Sheppard's ruthlessness and Weir's lack of morals.
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