The creators of the series have admitted that the episodes since the break were acknowledged as potentially challenging to the patience of the fans. They understood that these episodes, focusing on Sarah's character and barely advancing the overall season arc, would not appeal to the fans looking for answers. When even the producers admit that there's such a thing as too much character development, it's telling.
In essence, the focus has been on Sarah because this is the first time she's killed a fellow human being. It was bad enough to see John do it in the season premiere, and then try to help him deal with the psychological consequences. Sarah is having trouble sleeping (expressed in her drug-induced hallucination of the sleep clinic), and knows that it's affecting her ability to protect John. Similarly, she's still worried about her health, and the notion of Cameron becoming her protector. (Interesting how, in her dream, Cameron is much more overtly flirtatious with John.)
While the episode structure is quite clever, and manages to hide which version of reality is "real" until the final act, it does seem to be a bit too convenient in the long run. Sarah is feeling guilty about killing Ed Winston, despite the fact that it was clearly self-defense. This time, Winston is a much more potent threat, and tortures Sarah relentlessly. It's almost as if this incident is meant to give Sarah a reason to absolve herself of the guilt by giving her a damn good reason to kill Winston without remorse.
That psychological shift is only viable if it is expressed in other ways in the future. Sarah has to come back from this experience with more dedication to her mission, and she has to act on her concerns. In other words, she needs to be proactive. This shouldn't be reserved for positive developments, either; she should be willing to take draconian measures when she deems it necessary. Her apparent lack of remorse for shooting Winston in the head should mean a colder, more clinical Sarah.
If that is going to be the case, then this unofficial "Sarah Trilogy" (which makes little sense, given her name is in the title of the show) will eventually prove valid in retrospect. In fact, the real problem is not that this process took place, but rather, that it took place right after a long winter break, just after switching to a far more difficult night. The switch to Friday nights was always going to challenge the ratings, and this particular direction, however temporary, only contributed to the slide. This could be a case of doing the right thing, even the necessary thing, at the worst possible time.