During the events of the Morrowind main questline Vivec helps the Nerevarine to defeat Dagoth Ur and presumebley knows he is going to destroy the heart of lorhkan after all he gives him wraithguard.... so surely Vivec would destroy the Ministry of Truth with the last of his powers to prevent mass death from the resulting Red Mountain explosions etc. So either Vivec just had a major brain fade or just said fuck it and decided to let everyone on Vvadenfell die.