The guy in the beginning, Gus, was Stabler's dad's old partner. Stabler asked him about the circumstances around his dad's Combat Cross in an earlier episode and if I remember right made it clear he heard that it was staged from Frank Donnelly. Coming back and confronting Gus about being crooked and a liar and telling him "I'm doing my job" must have made it clear to Gus that Stabler was an honest cop investigating corrupt cops and, being in the Brotherhood, he had to be doing so to bring them down.
Unless I missed something, it seems like a little bit of a leap for Gus to go straight to calling Donnelly and telling him that Stabler is undercover with 100% certainty, but that seems to be what happened.
As for the rest of the episode, I think they made it clear that Nova was the one who killed Webb. I agree with illdoc above stating that Cassandra's line about Webb not wanting to leave his "daughter" without a father pushing her over the edge. That was actually one thing that felt rushed to me. It was just in the previous episode that Nova's brother Derrick confronted Webb with a gun accusing him of murdering their father. I don't think that Nova shooting her brother in the leg (or wherever she shot him) should have immediately cleared her of all suspicion in Webb's mind. I really don't feel the scene accomplished much.
I'm also curious as to how Nova can simply turn in her badge and leave town. Certainly she's going to have to testify against, at the very least, Cassandra Webb and Leon Kilbride, no? If they already know Cassandra didn't kill her husband, they have to look into who did, right? I'd hope to see this addressed in early Season 3, but it also seems as though they wanted everything wrapped up so they can start anew this fall. Who knows?
