Yeah, I don't think "couldn't smack them down" is accurate, but the fact that it wasn't clear cut whether or not they actually had some small valid authority over him gave Alfred pause about whether or not it would be an appropriate action.
To make a metaphor, I think angelic grace is the original power and framework forming the prison, evil B.O. helps to power it and keep it going (like those finger trap toys where pulling harder actually works against you), and the genus loci is the user interface for utilizing it.
I'm close to that, but without tapping the Well to power it. I don't think there's a need for that if the build with the Grace was done correctly, and if it was an archangel's Grace.
If Michael borrowed a jumbo jet to use as a pen light, then I think Merlin borrowed a jet liner, tore the wings off, shoved the fuselage in the ground, stuffed it full of inmates, and used the engines to eject their oxygen up and out so they're too weak to try to escape, took a pre-existing shepherd of the land and gave it control in the cockpit, and slapped a headset on it, told it to obey whatever the person on the other end said to do, and gave it the ability to pick who was worthy of holding the other headset.
Admittedly that's being a bit literal with the analogy, but still.
Meanwhile the former pilot is Out of a job based on the Choice he made. All he was left with was the drink cart, so he wandered off and opened a bar.