The problem is that Elidibus admits that the Convocation's understanding of the Final Days "was the same as our own", which means that whatever information Hermes provided to them was...non-essential. He wasn't even able to pin down dynamis as its cause.
He is not going to be sabotaging anything if the Convocation was aware of his behavior, and they were apparently already accounting for dissidents like him considering that they had a bureau of justice (Which Emet-Selch actually mentions that he might have to get involved when he first hears about Kairos due to recognizing the potential threat it posed).
And yes, they may have hypothetically run into/created other threats that would've ended them, but by all accounts, they had already kept things together for a long, long time, and considering how easily both the Nibirun and Ea were convinced that life was still worth living by the end of the Omicron quests...I don't think a race of intellectuals like them is ever going to collectively agree that erasing themselves from existence is the best course of action.
