a metaphor for co-habiting couples?
the way the show actually plays now seems to me to be a pretty straight metaphor for a couple living together unmarried. they weren't allowed to show any sex, but very often the show is open about the fact that Tony and Jeannie are indeed a couple (she's even referred to as his girlfriend several times), and in reality everyone knows when you live with someone that's what you're doing.
i think that was a way to kind of get around the censors and play into the new social mores of the late 60's, when more people were starting to live together openly, even though the older generation still frowned on it. for example, they could never have done that premise even five years before it debuted