I expect someone snarky to come along and say "The fix is to not play Classroom Curses," but:
Page 25 of the rules lists what happens when you run out of various components. Darkness tokens aren't explicitly called out, so they fall under Other Tokens:
All other tokens are unlimited. If players run out of a token type (such as horror tokens), they should use a suitable replacement (such as a coin) to mark such an effect.
You've got plenty of horror tokens, and there isn't another reason to place them in rooms in this scenario, so they're a good replacement.