Once Clyntahn turned on Trynair, I felt (quoting Sherlock Holmes) that "The game was afoot."
Clyntahn threw down the gauntlet to the surviving members of the Go4 when he put Trynair through the Punishment. So whatever plans Duchairn had up his sleeve, (pun intended!) he needed to implement them quickly. Fortunately for him, the riots set off by the Inquisition's excesses in Zion finally allowed him to pull off his coup. (Although how Clyntahn failed to account for the major army training bases within a day's ride of Zion is beyond me.) I suppose that when you think you have absolute power it's hard to see that others may not believe in your "invincibility."
Magwair grew up a lot and I don't think that Clyntahn realized that, or ever considered him a threat. He was too busy peering over Duchairn's shoulder to notice where any armed opposition was likely to come from.
In the end Clyntahn received the sort of death that was politically acceptable to both sides, but not the sort we'd have liked
him to suffer. I wanted him to go through the whole rigors of the Question and the Punishment, and then get the Great Reveal after his tongue was cut out to show him that his entire belief system was a lie and a hot place in Hell was waiting for him!
I've been known to be a bit vindictive though ...