That's what bothers me I guess. The Enclave was getting steamrolled and just let the Citadel operate. The only thoughts I had were that they still felt they could win somehow and claim the Citadel and its pre-war tech or they werent able to get the strike overhead until seconds before the LW bursts in and goes demigod on everybody.
I'd imagine they were saving the shots because they were quite confident of steamrolling the Brotherhood without needing an orbital strike to do so.
Remember, that satellite
cannot be reloaded. They only get a few shots, and every one has to be made to count as much as possible. Their conventional forces were enough of a match for the BoS that they didn't see the need to deploy a satellite strike on the Citadel; unfortunately, they failed to account for the Lone Wanderer.
Furthermore, as the majority of Brotherhood troops would have been in the field prosecuting actions against the Enclave, destroying the Citadel would not have eliminated the threat of the Brotherhood's ground forces at all.