No, the current Church knew. There were priests in the council arguing not to piss off Shu, they were just shouted down by the other power/glory-hungry Priests. The power-dyamics/internal-politics of the Church were desribed at length in the WN.
Even the greatest Miko of all time (and the last Miko, coincidentally) could do nothing against this bloodthirsty Church's stupidity.
Her foresight power wasn't "misinterpretable" like the Prophecy Miko here. Or subsequent Mikos who had future-telling power like "paintings", "poems", "music", "intuition", or "tarot cards" in the hundreds of years between then and her birth. The last Miko's powers were literal bidirectional time-stream knowledge, and hypothetical future viewing. And she saw all futures leading to ruin, thanks to the Church's arrogance no matter what she said or did.
Couldn't fight Shu or win (or other "Demon Kings" [sic: Shu/Hawkeye's plan to let Church become arrogant and destroy itself]). Couldn't run away (and survive). Couldn't stay (to stop the Church). All futures Church running head-first to ruin.
As a result she became incredibly despondent, didn't do anything, and didn't foretell any futures to the Church when they came to her (prison-like) room and asked. Always saying "It's meaningless."
In the end, the only path she saw where she could survive (along with some of humanity), was one where she slaved for the Church, until faking her own death, and running away/hiding (with a few crew survivors) in Laputa-esque warship above the clouds, while the world SCP-XK'ed itself with "Giant Warrior" taboo weapons, causing epoch-long nuclear winter.
So no. They knew the meaning of the "wooden door", and either (a) refused to, or (b) were psychologically incapable, of accepting it. Just as the author capstones with the Final Miko princess.