I was fine with her being apologetic. Not in a "I should have been with you" sort of way, which is not how I took it, simply in a "I've ruined quite literally everything" sort of way. Otherwise though, I definitely agree. I didn't mind the Grimoire plot, apart from increasingly shrinking FF7's world, but it fit with increasing the significance with Chaos, which is fine. And she didn't really kill Grimoire, the stagnant Lifestream just broke out of the thing. Certainly something for her to feel bad about, but she didn't murder him.
There were two moments I appreciated Dirge showing of her. 1) Her response when Vincent is protesting what she and Hojo are doing. While in other scenes they had a tendency to make her a bit flaky, she was resolute here and it absolutely fit with what we know. As Splintered said, she cared about science first. I like that she finally gets annoyed with Vincent and tells him to come out with it. And all he can muster is "Are you sure?" Which is a reasonable question, and she answers, "If this only concerns me, then yes, I am sure." I really like that scene, it's one that truly benefited her character. Whether by "if it only concerns me" she's referring to Hojo's say or that she believes this experiment is for the greater good, I think it legitimately adds depth without cheapening anything else about her.
2) Her breakdown regarding Sephiroth. For awhile her breakdown is about Vincent, which is mostly just annoying. But when it comes to Sephiroth, "Let me see him! Just once!" THAT'S the point where you can actually feel for her, and with the words flashing all over the screen and her sitting on the floor saying "Jenova's cells..." I think it's clear that this is where she attempted to kill herself and failed due to Jenova. This was another pretty powerful scene that meaningfully added to the narrative.