It's called "back-billing" and Thrifty (DTAG) corporate definitely used to have this ability with their franchisees. Unfortunately, since things have switched over to the Hertz system and procedures, it seems (from my experiences and understanding) that Hertz corporate is no longer willing to back-bill franchisees and is referring all customer service inquiries about franchised locations directly to the franchisee for final resolution.

Good luck to the OP, though. I agree the best chances of getting this resolved will be if you did go ahead and pick up the rental and pay the higher amount and then file a customer service complaint--and failing any productive fruit from that, escalate to the VP level (contact info here may be helpful).