If Ubisoft had said "sure the cult is right about the end of the world, but they're still morally reprehensible" and then devoted a chunk of the game to you gathering people that you saved in the apocalypse. then it would be ok.

In my mind, this could have been done by just letting us kill Joseph in the bunker. He still gets to go on about how he was right, and we still get to reaffirm that even if he was, he was still a piece of shit.

I dunno if they should have let you save everyone though. That might have been a step too far. If they did, then perhaps if Joseph had a bunker underneath his church that everyone huddled into as the bombs fell, that might have worked. And if they still wanted that monologue option, the second you get into the church, a bliss gas trap activates and the rest of the sequence goes on as normal with everyone tied up in the background.