But YOU made the choice. I don't care what the mod indicated that you should do. It was still your choice. So... it's on you.
Now, unlike in real life, you have another chance. You can go back and change your original choice. BINGO! Klaus is resurrected! It's a miracle!
You see, this is a game, where you not only have choices, but you can change your mind and make different choices. That's what saves are for.
As for you not having finished the game - no one has. Not even the developers, since they're still working on it. Nobody here knows what will happen, but it does appear that we are nearing the end. But if you want to know what happens, I'm afraid you will have to endure at least one more big download to find out.