Keep in mind Harmonia's #1 goal has always been acquiring all the true runes. So I think they captured the FC for the rune as much as for being an insubordinate. I was always under the impression that it'd be pretty hard to keep a True Rune bearer as a generic prisoner. I assumed they took it from him like Luc takes Geddoe's Lightning rune or how Windy was going to take Ted's rune.
So he was a bandit, at some point acquired the rune, used it for personal gain, realized heroic impact he could have with it, fought Harmonia, was captured and the rune was taken, fire bringer freed him and they retook the rune on their way out, then he saves the Grassland. I would think if it was intended Harmonia had the rune before the FC ever did, I can't imagine how he'd stumble across it as a common bandit.