WoTC interfering with games is not new though. Obsidian was infamously blocked from implementing the ability to end the Wall of the Faithless in NWN2: Mask of the Betrayer by WoTC, which was awful since so much of that campaign revolved around what a horrific cosmic injustice its existence was. But they *did* let you eat Myrkul's soul. Fast forward to 5e and here we have references to the Wall quietly scrubbed from the books and Myrkul spontaneously reappearing and back in the spotlight. WoTC.
I think the dialogues for the cut NWN endings you can read with the toolset. In one ending you could use the true name on the big bad to make him your companion as you wander the planes.
And I am not surprised WotC prevented the best good MotB ending. Yet in the evil ending you are allowed to kill gods, somehow that was not a problem for the setting.