If nothing else, the reconsideration given to the final six episodes of the season has given the final stretch of the arc a bit more cohesion. The drawback is that not much has happened since the revelation of Tony's apparent betrayal. The story the writers have chosen to tell to end this latest no good, horrible day requires a bit more setup than one might have anticipated.
On the other hand, it's still very much a part of the story that they had intended to tell from the beginning. This isn't like the third season, where it was all too clear when the writers decided to abandon the original plan and pursue a different course. The transition has been fairly seamless, and it really does feel like the writers just wanted to rethink the endgame. Without knowing the original plan, it's hard to say if the revision was justified or not.
The situation does, however, allow for the ongoing debate regarding tactics in counter-terrorism. In comments for the previous episode's review, some took exception towards Jack's decision to use the CTU servers to work up profiles on Muslims, calling him a racist fascist. Jack partially answers that challenge early in this episode: Jonas Hodges specifically mentioned using Muslim terrorists as a front for the domestic terrorist operations. Jack wasn't the racist; Jonas and his fellow terrorists were.
Yet this episode also demonstrated the thin line that Jack walks in the name of preserving his country's security. Whether due to his condition or a lack of information, Jack is a bit over the top with his tactics with the imam. Later, when discussing Tony's likely strategy, he says that it's what he would do in the same situation. Jack is hardly perfect, and he knows that he crosses the line when the situation appears to call for it.
In the world of "24", extreme interrogation methods almost always work, and they always seem to be used on the individuals with the information needed. With that kind of certainty in play, it comes down to pragmatism. When you know a method will work with a high degree of success, and there are no other short-term options on the table, the alternative is to allow American citizens to be casualties out of inaction. As Jack says to Janice: "Do you have a better way in mind?"
This is also a matter of public debate in the real world, where the stakes are just as high, but the success of coercive tactics are less cut and dry. Several sources within the intelligence community concede that extreme measures rarely produce actionable results. That being the case, the pragmatic approach is that alternatives must be developed and explored.
The realities of "real politik" force all nations, whether they want to admit it or not, to have counter-terrorist organizations that use borderline or even illegal methods to achieve the goal of protecting their country's interests. To put it simply, it's hard to stand on the moral high ground by refusing to counter illegal and heinous actions conducted by terrorists with their own methods when they're killing you. The trick is where to draw that fine line. "24" demonstrates how hard it can be under the best of circumstances.
It also makes the case that the right people have to be the ones willing to take those extreme actions. Olivia Taylor is not that person, especially given that she is the acting Chief of Staff. But she also doesn't consider the possible consequences of her actions. Why didn't it occur to her that setting up this assassination of Jonas, then backing off, would just make her (and by extension, the administration) the perfect target for blackmail?
The bottom line is that this episode continues to make the case for the necessity, within the "24" universe, for an organization like CTU and an operative like Jack Bauer.