Lots-a-luck. Don't mean to be smart, but when the warm moist air in your house rises and hits the cold window, the basic law of physics dictates that condensation will form. Hence, your own private rain. Theres not anything you can do with the present set-up. Go back to the contractor and see if he will change it out to a double glazed skylight. I think any mfg. should be shot for selling non-double glazed skylights.
GOOD LUCK, Bill