Welcome to the site!

I'm sorry to hear about your snake, but it sounds like he's just a little stressed and needs time to get used to his new environment and the mite treatment. I wouldn't worry too much about his eyes. If the mite treatment is intended to be used on him, getting a little on his eyes shouldn't be a problem as they are protected by a clear scale like the rest of his body.

However, I would be concerned that you haven't completely eliminated the mite problem. If they come back you might want to try and locate a product called provent-a-mite and follow the directions on the can (you spray the enclosure and let it dry before placing your snake back inside). This treatment usually works much better than the topical mite treatments.

Good luck!