When a series is structured around a phenomenon like time travel, it's very important to set down how that time travel will work. Are events effectively pre-determined, with free will being an illusion? Or are events fluid, so changes to the past create a "new" reality in the present? Most of the problems emerge when writers try to work their magic in some middle position. It almost never works; shows like "Heroes" suffer from that fast and loose treatment.
Time works in a very specific way on "Lost", and that makes things a lot easier for the audience and, from a certain point of view, the writers. In essence, events are fixed. Everything that happens was always going to happen, including traveling through time. There is no such thing as unintentionally changing the past and thus changing the future. Even so, the nature of time does allow a small measure of fluidity; events will happen as they must happen, but the circumstances might shift and change.
Daniel was definitely trying to head off the effects that Desmond suffered in "The Constant", but it's odd that Charlotte seems to be the only one experiencing the problematic effects. The obvious difference between Charlotte and the rest of the tribe is her origin: she comes from the island herself. That runs counter to expectation; one would expect those born on the island to be safe. This does, however, bring up some interesting questions about Desmond, and whether or not Charlotte's reaction suggests a similarity of origin.
Oddly, the editing made it seem as though Desmond only remembered his unusual conversation with Daniel, back during his Swan Station days, after Daniel actually had the conversation. That appears to violate the rules, but it could be the result of the juxtaposition of two events outside of the context of their time. In other words, that suggestion could be deliberately false. On the other hand, it could point to Desmond's unique nature as someone with more "fluidity" in time than most.
Overall, it would appear that the tribe ultimately arrives, as anticipated, in the 1980s Dharma Initiative era, right in the middle of their little war with the Hostiles. Being unknown to both sides of the conflict, they are naturally seen as a problem by both. This makes things a lot more difficult and dangerous for them, to say the least, but it also helps to explain why there were so many subtle hints that a third group had been around on the island at some point.
Back in the future, the Oceanic Six is not having an easy time of it. Setting aside the focus on Hurley for a moment, Kate's meeting with Sun is definitely going to be a problem. This alerts Sun to the fact that someone is using Aaron to manipulate Kate, and that means Widmore is likely to gain advantage against Ben.
That's a problem, because Ben is apparently working on a very short deadline. Never mind that Mrs. Hawking from "Flashes Before Your Eyes" makes another appearance, thus reinforcing the notion that Desmond's part in the story is rather important, but she seems to have a method of tracking the island in space and time when it has become "unstuck". That short timeframe strongly suggests that the race to get to the island and the concurrent battle against Widmore's organization will not take the entire season.
The bulk of the Oceanic Six action, however, involved Hurley and his crisis of conscience. This was good to see, because the season premiere and the new format threatened to undermine some of these character-centric elements. Instead, despite all the various plot threads and implications at play, Hurley's psychological anguish is front and center. In fact, this adds to the explanation for his mental breakdown.
The writers did a great job of setting up the major complication of Hurley's pending incarceration over the course of the episode. Should Ben have expected more cooperation than that, under the circumstances?