Well, I've never had to treat a snake for mites, but my guess is that it would put the snake under more stress, which is pretty counter productive to getting a snake to eat for the first time.

Then again, if he does eat, you'll risk regurgitation during the treatment if you stress him out too much as well.

Personally, I'd focus more on trying to get him to eat, and if he eats, let it settle before you treat(just because it's been a while since feeding). If he has mites, an extra day for the food to settle isn't the end of the world.