The fact that by the book Mac knew about Don killing Jess' killer and decided that he wasn't going to do anything about it bugged me. Don't get me wrong, I love Flack, but when TPTB decided to have him pull the trigger it really screwed up the show IMO.
It would have been obvious from the CSIs examining the scene that the dude was shot unarmed when he was down and obvious that it was Flack's gun that fired the shot. It never made any sense to me that the only thing that ever came from it was Flack feeling guilty about it.
Actually we don't know exactly what
did happen. When last seen, Cade's gun was on the floor next to him, within his reach. He could have grabbed for it. That's unlikely given Flack's subsequent comments and behavior, but it could have happened.
When he shot Cade, here's how I saw it played out. Flack would make a statement to the effect that, "When I came into the room I saw Cade down on the floor on his back. He had a gun in his hand. As I moved toward him I told him to drop it. He pointed it at me. I shot him." Or he could have said, "When I came into the room I saw Cade down on the floor on his back. He had gun lying next to him. As I moved toward him I told him not to move. He grabbed the gun and I shot him." There would be enough evidence to back up either version.
As for Mac's "knowing", well there's "knowing" and knowing. He "knew" (thought) based on what
could have happened, knowing Flack's character, and seeing Flack's obvious guilt. Although the guilt could have been explained away that it was just grief about Jess. The actual, provable, collectible evidence from the scene must have backed up whatever statement Flack gave. I'm sure Mac didn't tamper with it. Unless Flack confessed or an eye-witness showed up, "knowing" wasn't enough. (And Danny wasn't a witness. He didn't arrive until after it was over.) That's why Mac stopped Flack from saying too much in "Cuckoo's Nest". He didn't want what he "knew" (thought) to become knew (provable), and a confession would change that. As for the "limbo" scene, that was just in Mac's imagination. Since it didn't really happen, it doesn't change things.