I think that "good" kids (good being defined by good grades, no trouble-making, etc etc etc) deserve a little time off every now and then.

If he's been in attendance for the majority of the class (sans any sick days, etc.) then I don't see where one day will make a difference. And, it's not like he was goofing off... he was working on a school related project! (Kudos to him for that will power! I think I'd have tried to sleep or watch tv! )

If you're happy and confident with your decision, then I think it was the best choice.