I was wondering if any of you knew a way to write to a batch file ingame. The main reason is to fix faces of modified NPC's through the setnpcweight command.

Papyrus doesn't "talk" to the console which is all the batch files can execute, so no. You could, however, Alt+Tab out of the game, edit your .txt, Alt+Tab back in, then execute it and the edits will work without reloading...