The fact that the study was on children certainly doesn't help the validity when applied to adults, but I think you're being overly risk-averse. Melatonin's mechanism of action is pretty well understood, and it occurs in the body already. The long-term effects would have to be very bad to outweigh the advantages of a regular sleep schedule and an extra hour of wakefulness every day. That's assuming melatonin works, of course.
Endorphins are chemicals that occur naturally in the body, with a mechanism that is pretty well understood. Yet taking opioids regularly is not good for you.
You cannot assume health-benefits simply because it already occurs in the body.
There may well be benefits, but they must be proved independently of simply understanding the natural mechanism.
Full essay: http://www.gwern.net/Melatonin