Episode Specific Spoilers
What is a serial killer with a disobedient protege to do? If you're Dexter, you carefully scrutinize your options. This is one of the characteristics that separate him from ordinary murderers. He has a process.
Option 1: Kill Miguel. Although it's a sufficient comeuppance for the death of Ellen Wolf, Miguel would be a hard man to kill. Or rather, he'd be a hard man to get away with killing. He's high profile, close to Dexter, and perhaps most importantly, Dexter would have to fake grief.
Option 2: Get Miguel out of his life. Not an easy task considering how clingy the guy is.
Option 3: ...more Dexter