If you already have MC29 running and you want to fully remove MC28, use the following commands in the terminal...
sudo apt-get remove mediacenter28
Then...
sudo rm /etc/apt/sources.list.d/mediacenter28.list
You also might need to remove the mediacenter29.list if you're using installJRMC, if you want to start fresh. Though if you've already added MC29's repository manually, there's probably no reason to use installJRMC as MC29 is already installed.