Frankly I feel like if we didn't kill Vivec in 686,432 alternate realities then there would have just been trouble. Man was already getting too big for his britches before the playable part of Morrowind even opens. If he was just left to his own devices without the Nerevarine to interfere probably nobody would have ever lived a peaceful life again. Last thing we need is an immutable God that also can't keep it in his pants and has nobody to answer to that is a credible threat to him.

Only reason Vivec didn't cross the sea to be known in Skyrim is that he knows damn well the Nerevarine took his ass out 686,432 times in alternate realities and that Nevvie is still lurking in the shadows staring him down from the safety of the Creation Kit. He makes one wrong move and I'll fuckin delete his UID, erase all evidence of his ever existing, 'cause Vivec is not the only one that learned what CHIM was, motherfucker.

It's entirely possible to kill Vivec and still beat the game, it just requires a bit of a detour.