In the end, all went according to Ater's grand scheme.
The Nobles, Deserters, and Dragons were all eliminated on the same day—each taken off the board in a rather spectacular, yet natural way. As long as the narrative that was spun remained effective, there would be no problem.
The Nobles were killed by the Deserters, hence getting rid of them and the annoying authority that they wielded in the Alliance.
The economic and social impact their demise was going to cause made the Royal Council silently celebrate. The dissolution of their estate, the confiscation of their assets, as well as the massive creation of spaces in the South, would allow for a greater quality of life and less cost for those who lived there.
There would also be less resistance to the governance of the Royal Council.