By that same logic the game shouldn't end because you put a lot of work into playing it.
There's literally no content for Bao-Dur in the end-game. The easiest and most commonly accepted solution is that he dies (based on the little evidence we have).
Of course, there's nothing forcing you to download a mod where Bao-Dur dies. Also, no one is banned from making a mod where Bao-Dur lives.