There is a theory/argument that the entire situation was a setup. That the Iconian gateway is a fake, the renegade Jem'Hadar never rebelled, and all of it is part of a "false flag" operation intended to get close to Odo.
The basis for this being it's generally believed it's in this episode where Odo is infected by the virus which forces him to return to the Great Link in order to be judged for killing the fellow Changeling in season 3's "The Adversary."
In this respect, when the Jem'Hadar First murders this version of Weyoun, it's not an indication of his autonomy and ability to go beyond the control of the Founders and Vorta. Instead, it's probably part of his orders to kill the Vorta who's a carrier of a Changeling disease after he completes his mission to infect Odo.
Interesting to note: Odo is also carrying the Section 31 virus at this point too (i.e., the writers/producers have stated that in their minds he was infected to be a carrier during the "Homefront" and "Paradise Lost" 2-parter on Earth). And by pulling him back to the Great Link, Odo infects all of the Changelings with it.
