I still think Tony is a double or triple agent (I've lost track). All the genuinely "bad" things he's had to do to "good" people, he looks very sorry about, but it's necessary to keep his cover. I think the last three years he actually INFILTRATED all these high-up bad guys and has had to do horrible things to maintain his cover.
After watching Jack have a seizure in front of him at the end of this episode? I don't buy it. But all remains to be seen.