There was on-set drama — another altercation with one of the show’s writers — but they didn’t kill off the character, they came up with a good reason for his exit.
In this case, Jack may get a hero’s exit from MacGyver, as opposed to being killed off or exiting in ignominious fashion.
They also left the door open for the character, which … is that something they might do for Jack as well?
It’s kind of like how Criminal Minds wrote off Thomas Gibson’s Hotch.