They weren't genuinely happy living with the losties--they bickered and fought and Rose was something of a shrew.
I definitely agree with you that they still had some healing to do during the early seasons (like most of the characters). However, I don't think living with the Losties was the core of their problems. In fact, I think it was a mistake for them to live as an island when the point of the show and the finale is that everyone needs help and to be part of a family, which I definitely think they were for the first 3-4 seasons.
Why would they want to return to the people that brought that out in them?
Bernard and Rose's real issues weren't caused by living with the Losties, their problems, like everyone else's was inside each of them. Yes, they worked through them to find real peace, but I think it had little to do with being with or apart from the Losties. In fact, I'd argue they were a bit like ostrich's that hid their head under the sand and wasn't part of the struggle for good in a battle that had real consequences. In that way, they were sort of cowards to some degree.
They were much happier alone.
Sure, people who live in denial live that way because they believe they're happier that way. Still, ignoring the struggle against evil doesn't mean that there isn't one. Had Flocke gotten his way, they would have sunk with the island, drowned and evil would have been unleashed on this world and all's they did was bury their heads in the sand and say 'we don't want to be involved'.
And they were alone for years, doing everything they could to avoid re-integration into this family. They spent what, 90 days with the losties and three years living alone?
Yeah, I'd say that's a fair assessment.
Rose really, truly believed she had cancer and was dying. She experienced it ... every perception that goes along with cancer, all the pain and fear. Bernard, too, from his POV. Had Desmond not intervened, who's to say what would have happened to her?
Well, obviously we're just guessing here - and as an aside I really don't think the writers wanted us to examine the rules that govern this afterlife staging area - but the cancer would never actually claim here and she would struggle with it till she worked through it or just kept struggling with it forever.
Sayid deemed himself unworthy of Nadia. That he saw Shannon as what he deserved is more telling about Sayid's self-view than how he perceived Nadia.
Or Jack's wife, whatsername he operated on. Or Christian's wife. Or Christian's lover. Or Kate's husband, Kevin. Or Kate's boyfriend, Tom. Or Libby's husband. (Was she even there?)
Libby was there. And according to who was in the church, those people who weren't there weren't who the people they cared the most about.
I hear what you're saying about the church scene being for the fans and not for the story and to a degree I can buy that. Still, I think the whole notion that these people who spent the first 3-4 years together as a family, struggling to work through everything the island threw at them bonded with those particular people in ways that they didn't with anyone else and that's why there in the church. Christian said as much when he said that Jack's time on the island was the most important time to him and those people would naturally mean the most.