I'm disinclined to believe Fandaniel was some secret death cultist all along, for one particular reason. Specifically, the rest of the Convocation had access to his memory stone for 12,000 years. Given the abilities Mitron had on display during Eden's Promise, I can't imagine it would be difficult for the likes of Emet-Selch to sort through Fandaniel's memories in a similar fashion. He wouldn't even have to suspect Fandaniel of being a traitor to do so—simply peering through them to make sure they're actually his memories would be a decent enough reason. It'd be nearly impossible for Fandaniel to actually hide his affiliations if that were the case, and that in turn would leave me wondering why they bothered to ascend him to begin with.

I mean, there's hubris and then there's "we knowingly raised up a man who had been plotting the downfall of our entire world because we thought a stern lecture or two would keep him from doing it again".