SMG was pretty upset about the direction Buffy took in S6. As far as I can tell, her main complaint was that Buffy the character lost popularity. At any rate, she didn’t think Buffy was “in character”, and she really shut down acting wise. Fury commented that it was impossible to direct her, so they just stopped trying to get anything from her S6 and S7.
She blamed Joss for that because he was off-set, working on Firefly. In Seasons 1-5, SMG was pretty active when it came to writing/directing, but her participation had a sharp decrease when Whedon made fewer and fewer appearances on the set of Buffy.
Also, I get the impression that Whedone was just plain, flat-out tired of BtVS. His real love was Firefly, and I think Angel took a close second at the time.
Things got really bad at the end of S7, when the future of BtVS and the whole franchise was up in the air. Angel was on the bubble, Firefly was already cancelled, and SMG was treading water. Finally, late in the game, she announced she was “hanging up her stakes” in Entertainment Weekly. As you can imagine, Joss (and the rest of the cast) wasn’t thrilled to hear the news from the press. (As an aside, Eliza Dushku pulled the same stunt when she accepted the role in Tru Calling. Before that, they were talking Faith spinoff).
So, tensions were high, and the writers (Fury, Minear, Goddard immediately spring to mind) pretty much had nothing nice to say about SMG. Allison Hannigan also had nothing nice to say. James Marsters never commented on her at all–he’s a firm believer in not speaking ill of his costars, so he just stopped speaking of her. But she still told Joss and announced publically she’d be willing to do an episode of Angel.
They planned for her to show up in episode 100, 5.12 You’re Welcome. That was the plan. And then she announced…in a magazine again…that she would not be able to make it. This infuriated DB, who up until this time never seemed to have a problem with her and even spouted off Angel/Buffy rhetoric on occasion. he called her unprofessional and it was very clear that he was not pleased.
Afterward, SMG tried to do some spin control and announced she’d love to show up for the finale if they asked her. Jeff Bell announced in an interview that they had already plotted the finale, and it would not include her. He further went on to add that they wrote The Girl in Question and they didn’t need her.
All in all, I don’t think SMG walked away from BtVS or AtS with a single relationship intact.