If the correctly appointed Empress and the Privy Council command, then I would obey, period. It is not my place to make these decisions. Pure Thought is the Instigator of Sin, Free Thought is the Begetter of Disorder, and Uniform Thought is the Way of Life.
Fortunately, I trust that they will never command anything like working with Omir or Kuvakei.
There is also a rather large difference between allowing an open heretic into a holy rite with the intent to corrupt said rite, and in that case make the Empty Throne Heretic’s nonsense a reality, and issues such as the open door policy towards pirates maintained by the Militia or the ongoing Amarr decision to work with the CONCORD Empires. And those members of the Praetoria who expanded their criticism past the EoM Traitor and targeted the Khanid Heir himself did in fact err badly.