Actually, a number of the USN C-9Bs were acquired second-hand (in some cases 4th or 5th). Almost all of the ex-airline C-9s were CF airframes similar to the new-build C-9s. The CFs came from Douglas with cargo doors and beefed-up cabin floors.
The cost of those aftermarket modifications to a relatively small number of Mad Dogs (in addition to acquisition and training costs) would be prohibitively expensive. The Navy is getting new custom-built airframes in a package deal which includes training and heavy MX.