The entire season has been about the questionable rationale for extra-legal (or flat out illegal) operations in counter-terrorism, and sure enough, the season finale brings a lot of those questions and concepts into focus. Surprisingly, while the writers have the character come to terms with their own answers to those questions, they leave the implications and consequences for another day. Which, given the time constraints of the format, makes a great deal of sense.
Tony's ultimate explanation for his behavior throughout the season is about as logical as one could expect for "24", but as insane motivations go, it actually sounds rather reasonable. It takes everything he said about his grief over Michelleâs loss and gives it powerful direction. More than that, it actually does more in a few minutes to add depth to the shadowy conspiracies behind President Charles Logan than all the nonsense in the fifth and sixth seasons.
It also underscores the larger structure that has emerged for "24". The previous three seasons drove Jack further and further into the darkness, stripping everything and everyone he loved and trusted away, until he was on his own. It only makes sense that the true masterminds of the post-Palmer terrorism would be harder and harder to find as a result, and that they would only emerge when Jack was on the road to his own redemption and restoration.
This also fits the overall message that, at least in the world of "24", organizations like CTU and operatives like Jack Bauer are necessary. Without the ability to step outside the legal confines of the intelligence community as it is known to the public, vital resources are lost and lives are at risk. It's easy to forget that Jack Bauer and CTU were originally depicted as black ops; they were never meant to conform to the same standards as the FBI or even the CIA.
For better or worse, Tony's plot was an attempt, however twisted, to fill the void left by Jack and CTU when they left the stage. Despite the fact that Tony clearly lost perspective on morality along the way, he was right to call out Jack on his self-imposed exile. The writing may have been on the wall for CTU and in terms of the Senate hearings, but it was out of character for Jack to run from the consequences of his actions.
Coming to that realization is a part of Jack's discussions with Agent Walker and Imam Gohar. When discussing the matter of torturing Alan Wilson for information about the rest of the domestic terrorist cabal, Jack essentially tells Renee that she should follow what her heart tells her. His heart tells him that he knows that he's breaking the law, and that his actions are often immoral, but that he couldn't live with himself if he let people die when he could do something about it. It's exactly what he was trying to tell Senator Mayer in the season premiere.
When speaking with Imam Gohar, however, Jack does confess that he finds it hard to forgive himself for the things he's done. Some will see this as unnecessary political correctness, right down to Jack's decision to call on Gohar. As usual, this is a short-sighted interpretation. Having no regrets is not the same as requiring no forgiveness. If anything, Jack's heroism is accepting the spiritual consequences of his actions for the greater good, even as that weight accumulates.
As for why Jack turned to a Muslim imam instead of a priest or pastor, it ties into what would be his only possible regret of the day: treating Gohar with so little respect for questionable reasons. Again, this will be seen by some (with agendas of their own) as pandering to those who demand religious tolerance. But as inelegant as the insertion of Gohar was initially, the follow-through has been sensible.