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.
I dunno, he could have left Jack to die but he got him some help.
I'm going with the double-gainer-triple-backflip-with-lemon-twist theory. I can see Tony being impulsive, getting mad at the gubmint and doing some bad things and then coming to his senses - his original backstory - but for him to be doing it all in such a calculated manner strikes me as wrong for the character.
Tony has decided that he's such damaged good that he can't rejoin society, so his final acts will be to take Jack's lone-wolf game and really go over the top with it. In the end, Tony knows his fate is prison or death (and it's clear to the audience it has to be the latter). Now that we know John Voight was merely a pawn in a larger game, it makes sense that Tony has gone off the reservation to expose the Even Bigger Fish in the pond.
I could even see this being a variant of what guys often do with guy friends - the almost unconscious game of one-upmanship. Jack shoots Ryan Chappelle? Tony is willing to take out a whole housing project of FBI agents for the greater good! Whether he admits it to himself or not, Tony is determined to finally beat Jack at his own Lone Wolf/Psycho/Self-Destructive Epic Martyr game.
Also, the Bad/Good/Bad/Good Tony theory will allow Jack to shoot Tony in the final episode (we know that's coming!) only after learning the truth and realizing that Tony is just an exaggerated version of himself. But he shoots him anyway - maybe that's the real reason why he does it? Double the angst! That's classic 24