And you would have thought there would have been more questions as to who she was with, what she might have shared with the person or persons she had contact with, etc. Given how suspicious people had grown of each other, and not without reason, it seemed off that Kara was so readily accepted back into the fold.
It really did. I did wonder if they were going to try and create a connection along the lines of Tigh becoming close friends with Kara as a form of over-compensation for the loss of Ellen, but then if they were going to use Ellen as a means of character evolution from Tigh, I'd have expected to see some resentment on some level from Tigh towards Anders over the death of Ellen, and instead other than briefly in Collaborators, the two were never on screen together. Failing to explain why Tigh and Kara are such good friends is a frustrating thing - just like not showing us the first encounter between Lee and Kara post-NC.

But she and Tigh hugging?!?! And, yes, that definitely needed to be explained, but there could have been better ways to do it.
I'd hoped that the deleted scene would explain it all, but instead it makes things seem even more bizarre - if that's not why they were suddenly so pally, why were they? In fact, given that in LDYB Tigh settles on NC on the eve of the Cylon invasion, how did Kara and Tigh even get to talk to each other, let alone bond? After all, UB showed that she'd been down on the planet for some time even at the groundbreaking ceremony.

Now, believing herself the screw-up, unworthy of love, who only leaves disaster in her wake - Zak died, in part, because of her actions and love for him - the only way she could see to protect herself and Lee was to do something so hurtful that he wouldn't and couldn't be with her. Of course, she didn't really think that plan out because she lost her best friend for over a year.
I think one of the reasons I resent having to try and rationalize out that scene is that I have trouble imagining Kara ever being terrified of Lee, and that's how most people explain it away. The problem with arguing that she considers herself to leave disaster behind when she loves people is that she evidently had no fear of that impacting on Anders - if the comments about her loving both of them (or even Anders more, as Katee seemed to indicate) are true, why is she not terrified of destroying Anders? In Collaborators, we see Kara moving away from him in what she evidently feels is the best move for him, but I have some difficulty with the idea that she's afraid of causing Lee harm... so she decides to put herself in a position to harm Anders instead. Alternatively, if it's a case of she doesn't actually hold Anders in enough regard to worry about compared to Lee, then I really like this theory.

The scene in EoJ was very problematic for me, probably because of my views on hypocrisy in religion. She couldn't get a divorce because she'd be sinning in the eyes of the gods, but she can be unfaithful to her husband and hurt three people in the process and that is OK? I wasn't happy with Lee in all this, but at least his plan was to leave Dee and stop the lies.
That's one of the big issues I have with that scene - the other being the reaction a lot of the fanbase had to TAB; it didn't seem at all out of character for Lee to call her on her offer to see if she was serious or not - she had already run away once, and then flat-out refused to commit to him again on religious grounds to go with whatever she'd been feeling/reacting to in UB - but a lot of people reacted as if Lee were just being deliberately abusive and pushing her away. I tend to agree with Boppy - I don't think it was at all unreasonable for Lee to basically ask "how do I know you're serious this time?" based on past evidence. If nothing else, I'd be inclined to ask the same question after all the whiplash-inducing changes of temprement characters seemed to go through in S3.