Why would McGee be the one paying Carmack back after all these years if that were the case? Can you imagine Walter White paying back Elliot for some long forgotten debt out of his drug money?
Regardless of whether or not McGee feels like he deserved to have been better compensated by id software for his contributions, he feels personally indebted to John Carmack for the money he borrowed.
And in the case of feeling slighted, while he could justify never paying Carmack back by saying that since Carmack was one of the founder/owners of the company that slighted him, this was just money Carmack owed him, he has not taken that tack.
It is possible to compartmentalize.