Sword of Spirit
Legend
Running a Dragonlance game...
You said it. You are running the game, not the player. Take command of the situation (politely). Straight up tell him that he can believe whatever he wants, and his character can believe whatever he wants, but it's your world, and you decide how alignment works. When he dies he can make his case to the Gods of Evil that he doesn't belong in their neck of the planes.
If he can't handle that, then that's his problem. Alignment in D&D is not something that can be up for debate as far as running the game goes, anymore than the weather. A player can argue that there shouldn't be a storm at that time of the year based on his understanding of the climate you described or whatever. But as DM, if you say there is a storm, there is a storm.
I'm not saying don't take player input. On the contrary, I generally make notes when players have suggestions or disagreements, and then consider it. More than half of the time I end up agreeing with them. But you can't let them take the game hostage.
If, on the other hand, I got the wrong impression from your post and this is just a friendly D&D philosophical debate, I'm sure there is plenty of good advice in the thread (I didn't read past the OP).