1. Get the follower's ID by typing in the console: help {follower's name} 0. You should see something like: NPC_(00013952) "{follower's name}." The number in () is the ID number needed.
2. Type in console: player.placeatme {ID number}. A duplicate of the follower will appear next to you after closing the console.
3. Activate the follower duplicate and tell them to go home or it's time to part ways.
4. Before they walk away, hit tilde to bring up console, click on the follower to get the ref ID (different from ID number).
5. Type disable to delete the duplicate.
I was under the impression that the death of a follower stopped the script, but perhaps it's glitched or something. The above should fix it, as the duplicate follower will still be running the follow script if it's still active on the original follower. You can end the script on a duplicate, and it affects the original. I've had to do it a couple of times.