Does being a somewhat dirty cop warrant execution? He even told Dex that he didn't have any plans to mess with Lumen.
One of Hary's rules is "Don't get caught"
He had to take him out.
Overall, Quinn knows something is up with Dexter. He may even still suspect Dexter of it still, and that Dexter covered for him. Odds are good its as simple as Quinn knows he can't touch Dexter because it'll track back to him and make him look guilty.
We'll see if next season dexter has the kids or if he's fully solo.