I have a recipe that calls for a scant amount of cloves. Would nutmeg be a good substitute?
In my opinion, yes. Go easy, you can always add more, but you can't take it away.
I would actually grab nutmeg for chili long before I would consider cloves.
I agree with @Jolenealaska and would also suggest allspice or cinnamon. The warmth of those, and adding cumin, does very well in chili.