I would be worried about long term damage. In 10 years you might be in a world of hurt from this. At the very least I would let your doctor know that you are doing this and see what they think of it.
Billions of people eat spicy foods on a daily basis without any issues. As long as he doesn't rub peppers into his eyes or bathe in hot sauce he'll be fine.
How many billions of people start their day by getting one Scotch Bonnet (or two smaller ones), two oranges, lime and a piece of ginger into a cold press and then drinking it in one go on an empty stomach?
No idea, but I often eat hot peppers in every meal of the day. I'd expect any possible issues to arise from chugging it one go and not priming the digestive system through mastication, but I can't imagine any real problems - after all, there are many types of drinks containing peppers.
If it hurts while just sitting in your gut that's probably a red flag that something about your digestive system is off.