We've seen three forms of mind-altering in the Safehold universe: the NEATS, the memory rewrites of the original colonists, and the partial memory recovery that created Sejin Khody.
We've seen hints that Chihiro and Schueler may have been behind the Rakuri and the war against the Fallen. What if some unscrupulous person, in addition to diddling with the memories of the colonists, decided to diddle with the minds of select command crew staff instead?
There may have been an opportunity to do so while the fleet was in hiding while Shan-Wei and her terraforming crews were working on Safehold. Would the rest of the command crew want to stay awake for the years that took, or would they stick as much of the crew as possible into stasis to stave off boredom? That might give Bedard and/or Chihiro the opportunity to meddle with the minds of the command crew in more subtle ways than the blatant meddling she did with the colonists.
In the interests of pure speculation, what if Chihiro had somebody program select members of the command crew to actually believe they were archangels and angels? Mostly, for Payter's sake, I'd like Schueler to turn out to be one more innocent victim instead of the monster capable of writing the book of Schueler. RFC has written any characters who are vindictively evil, and Chihiro might be the sort of person who takes someone who initially opposed his policies, minds crew them, force them to fight as his champion, and then saddle them with the reputation of being the church's chief torturer. Her certainly did a number on Shan-Wei, so why not a different sort of smear job for Schueler?
The real question is, would it serve the story better to have one or two truly evil people ablue to mind-warp anybody they please, or would it serve the story better if the command crew traumatized by the total destruction of their civilization were genuinely trying to do what they thought was the right thing?
) but highly unlikely. With all respect to Langhorne - i really like his transformation from the "mua-ha-ha"'ing megalomaniac to the tragic figure, who was unable to comprehend with terrible reality and enormous responsibility - but i doubt that he was mind-altered. It would simplificate the situation too much, turning him into the victim.