They should credit the amount back plus the overdraft charges, plus interest if you ended up getting charged any. Be prepared to fax them proof of the overdraft charges, of course. (I'm unfamiliar with this: they've overcharged my CC before, but I've been able to simply get them to reverse those charges without it costing me anything else.)

Points and the reward program have nothing to do with this. Make sure you are fully reimbursed the actual money that was charged. I don't think you should be demanding a bunch of extra stuff because they made an accounting error, but I also wouldn't let them get away with substituting points in place of a credit back to the card.