I agree that Laguarda's twist was good but if they had developed her character even a little bit more, it would have much more believable rather than having to swallow such a cut throat move in one gulp. She does come across as someone who would probably step on someone else's head but not to that extent. (Thanks for the reminder of Oz Pete, I couldn't place her for the life of me.)
Doakes is definitely dead but there's no way Dex could have killed him right there or else it would have made more of a mess and left things open. He did shoot Dex in the leg so that alone will make for Doake's disposal for sure IMO. Dex can fake a leg injury & make Doakes disappear but more likely he will sell a struggle of taking down Doakes to the feds to diffuse things for a while. Dex as well as Doakes himself have both painted a bad enough picture for Doakes so it shouldn't a hard sell. The only thing I can see creating a problem is time. Dex still needs to get rid of the cuban guy & keep Doakes fresh until he is ready to kill him so the story adds up. I find it hard to believe Doakes will not find a way out of that cage and keep the suspense up for just a little while longer. Regardless of what happens, Dex still has to come up with a better way to dispose of the bodies assuming this doesn't turn into the series "The Ex-Serial Killer Dexter."
I have no idea where it goes after Doakes goes away unless the entire situation leaves enough doubt with LaGuarda that she picks up where Doakes left off. Knowing her new found shady tendencies, she would probably make for a much more secretive cat & mouse game with Dex. I can't see any other way out. Of course having Lila out there is a real liability that must be dealt with at some point as well. Maybe she'll befriend LaGuarda at some point, both with intentions of getting back at Dex. I'm sure Dex will get back with Rita only for Lila to work non-stop in undermining the 2 of them...Dex can't kill Lila because of LaGuarda's growing suspicion...you heard it here first