The original post isn't entirely clear to me. It sounds as though, when you contacted the boat, they said you were okay, but the dive shop is requiring you to pay anyway? In that case, the ONLY situation in which it is legitimate is the one oly5050 posits. Having arranged trips myself, I know that there are few things that feel worse than putting the money down for a bunch of spaces, only to have the people who told you they were going turn around and say, "Well, maybe next time." I nearly lost $10,000 doing that once, and I will never do it again.
In all fairness, there was only one person in your party who really COULDN'T dive. The rest of you made the decision not to out of convenience, not necessity. Redoing your dives will require time rescheduled for the instructional staff and for the boat. In our dive shop, if you miss the scheduled OW dives, you pay an additional $100 a day for the unscheduled makeup dives, and those are shore dives. If the shop was out the cost of the charter spots, I don't think it was out of line to ask you to pay them.