The purpose of a carnet is to ensure that you export the vehicle when you leave the country. In addition, some, but not all, countries, stamp your passport to indicate you have brought a vehicle into the country with you.
So no, you can't legally leave the bike behind whilst you fly back to the UK. However, in Benin (or other countries on your route to South Africa) there may be local bureaucrats who are prepared to wave a blind eye at the regulations if you are able to suitably grease their palms, but that's something between you and them, and don't forget the risks involved.
Garry from Oz - powered by Burgman