The date on the note is wrong. The note itself references the rebellion and the events at the White Spire. If 9:40 were the actual date they would be referring to things that happen in the future. Also, in Asunder, word of the annulment reaches the mages after they've already moved to Andoral's Reach. This confirms that the Seekers who ordered the Annulment were belligerents from a rogue organization.
Everything in Asunder occurs in 9:40 as per the timeline provided by The World of Thedas. In the last chapter, Lambert muses the mages at Andoral will be crushed meaning the most likely timeline of events is as such:
Mages flee from the White Spire-Rivaini Circle annulled-Mages gather at Andoral's Reach, declare independence-Lambert declares the Accord void.
Technically, it could be like so:
Mages flee the White Spire-Reach Andoral's Reach-Lambert declares the Accord void-Rivaini Circle annulled-Mages declare independence.
But that is just overcomplicating it for no reason when even Asunder places Lambert's chapter after Andoral's Reach.
According to the actual law, as decided by the Chantry and the Rivaini government, no. I see no reason to debate it at without firsthand ACCOUNTS
or data suggesting they were a threat that required such a response.
According to Chantry law, which take precedence over everyone else in matter regarding mages except for the Right of Conscription, Abominations are killed on sight unless there is an option to remove only the demon.
Since the Rivaini mages refused to comply by the rules of the Circle, logic dictates they also refused to have their demons removed. Hence, by Chantry law, the Seekers had every right to kill them.