It wasn't a self-defense situation. What LaGuerta told Deb to do is murder her brother. Maybe she thought he deserved to be murdered, but if that was her reason then how was she any better?
Premeditated self-defence. Look it up, it's a real thing. If Maria believes in an hour, before they get to the police station, that Dexter is going to slip his cuffs and put a knife in her while she's driving... It's only sensible that she kill him now before everything comes to a head.