I just ... WOW, this reminds me so much of my character study, I was almost struck speechless the first couple of times I watched it. You can really see how their relationship has changed and grown, from the teasing, FWB-like arrangement to something quite a bit deeper. When he hugs her you can really see her opening up, probably far more than she has before, and actually almost crying. And to me, this is a level of emotion Kara would never have dared display in front of Lee before, lest he think less of her or believe that she's weak.
Now, I don't think he would, but at the same time, this is Kara we're talking about here. Up until the end of S3/beginning of S4, she didn't want anyone to see that she had vulnerabilities. This is why the character study was such an interesting project for me to undertake, because there was the ultimate vulnerability - having to function without hands, something that would be impossible for 99% of us - and needing to depend on the one person in front of whom she had always tried to appear strong. This placed Kara in the ultimate fish-out-of-water situation: as a wholly independent person, and as a person who projects a sense of independence even when maybe she shouldn't, not being able to do anything without someone else's help would present some real challenges to her and her character. Thus was the genesis of The Sound of One Hand Clapping, and to date I still consider it one of my best works ever.
Obviously my fic is not canon (heh) but some of the themes that it ultimately explored are, and I could see them running very strongly through the extended brig scene. Even just the way she looks at him, you can read on her face: "This is a person around whom I now feel comfortable exposing the most intimate parts of myself, something that was not the case before." And by intimate parts, I don't mean physically - clearly the sex was a factor long before Kara had even begun to wrestle with any of her demons - but rather mentally. Kara has always been much more comfortable with her physical body than she has with herself on an emotional level. Emotions are something she'd like to pretend she doesn't have or experience, because acknowledging them would open a whole other can of worms and for much of BSG, she can't deal with that. It's not part of her image, the image she wants to (and feels she has to) project. The fact that she is willing to open herself to Lee like she does in the brig scene is indicative not only of the change she has been through, but that their relationship has reached a much higher level than the one at which it began. Lee has here joined a very exclusive club: The Society of People Around Whom Kara Thrace is Willing to Be Herself.
I believe that there are probably one, perhaps two, other members of this club. Maybe three if you're willing to suspend disbelief a little. First would have to be Zak Adama. I think Zak was the first person to penetrate Kara's mental shields, and to draw her out to an extent that she was comfortable sharing herself. We don't know exactly how long their relationship lasted, but my suspicion is that it would have to have been at least two or three years, because no way was she going to trust him any quicker. Helo may be another. In my personal canon those two are best friends, and he probably knows more of her than just about anyone else. I'm not as sure about Admiral Adama, although there are definitely indications that they share a very close, nearly familial bond. The question of whether she would be willing to let down her guard around him is a little more difficult to answer - we've seen such a situation once, at least onscreen. Perhaps twice.
Sam is not on this list, and he isn't on there for a very specific reason. What Kara was seeking in Sam - and honestly, this is no less valid - was simplicity. She wanted someone with whom she didn't have a history and someone who was uncomplicated and wouldn't ask too many questions. Sam won't try to get her to open up about her past, and he doesn't have the kind of history with her that Lee and Bill do. (Which, let's face it, is pretty fucked up. Heh.) He's just there, and she can accept his affections because she knows he isn't going to press. At the time in her life that she becomes involved with and marries him, that's what Kara wants. She doesn't want questions. She doesn't want uncertainty. She just wants stability, and Sam provides that.
I'll be really interested to see where Lee/Kara go in S4.5. As a Lee/Kara OTPer I'm obviously hoping that the brig scene wasn't their last interaction ever, but honestly, I don't think it will be. There's too much history and evolution built in there for RDM to simply leave it as it stands at the moment. (And if he does, fans will rightly complain that it's a knot that hasn't been tied up, and I will be PISSED.) What most fascinates me is that since their relationship is now at a much more mature level, they may be able to take it further. I'm not going to make any predictions about which relationship might be the so-called "endgame" of BSG - I love my two OTPs much too much for that! - but I think Lee/Kara will feature. Prominently.
Now, excuse me while I go rewatch this another 40505594303504565022 times. XD