Just thought I'd bump this up as I am late getting to this thread and this was a version of my thought, also.
Regarding why Casey and Lee were so upset during his testimony--she may really love her brother (in the way she understands "love") and she of course knows her defense team made him out to be someone who sexually assaulted and abused his own sister. Even if he was guilty of that, which I seriously doubt, it was a terrible thing to USE that in court to excuse her own indifference to (or relief in the face of) what happened to Caylee. Looking at him still trying to help her might have penetrated her narcissistic fog.
If there is a secret between the two of them, it may be that he (like the rest of us) feels he knows what Casey did to cause Caylee's death. Perhaps that is why he was willing to throw himself on the grenade to try to save Casey from the death penalty. One thing that interests me is that he said on the stand that he didn't want his sister and his parents to be in court--but that was a moment he could have said that he was upset that his sister was being tried for something she didn't do. He had an opportunity to say something like that, but he didn't. I think the DT didn't ask about the incest because I don't think Lee will lie about the big things. He will talk about a few old stains in the trunk, hedge about what he remembers, etc., but maybe like George (and unlike his mother) he's drawn the line against full-out perjury.