Tsaritsa's actions in the recent AQ make sense.
Nod Krai is officially a part of Sneznaya, an autonomous region of the Tsaritsa's country. Doctor literally turned himself into a god, which in itself directly challenges Tsaritsa's authority as a god of Sneznaya and Nod Krai, since there can only be one God and a ruler. Additionally, he endangered all the citizens of Nod Krai, who are the citizens of Sneznaya, by creating those domes across the region. It would be stupid and seen as weakness if Tsaritsa did not declare Doctor a traitor.
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Fighting back against the gods (HP, Celestia), something Dottore completely trampled on by trying to become one.
Hell, the delusions were entirely created as a middle-finger against Celestia deciding who gets to have godlike powers and who doesn't, so yeah Dottore basically trying to usurp the throne of a god to do whatever he wants is very much the main reason the Tsaritsa gave the thumbs-up to kill him.
But also, the Fatui has notoriously played dirty many times before, and we don’t know whether or not the Tsaritsa endorses it.