Right, been reading my user manual for the DVD version of the MFD2, and there are possibly a couple of things you can try.
Firstly, the add on tuner is controlled by the AUX input. This is activated or de-activated as follows (assuming you have access to this menu)
Press the CD Button, and then on the lower right hand side press SET UP to open the main AUX menu.
From here you have a choice of activating or de-activating the AV or AUX sources. For AV you will have the choices - A+V, AUDIO or OFF. For AUX the choices would be - AUDIO or OFF. Turn the AUX to OFF, this should de-activate the tuner and give you control back over your CD player.
The only other option I can think off (short of taking the unit out and unplugging the tuner, is to reset the MFD2 to factory defaults. I'm not sure if this will wipe your pre-sets, but that's no real big deal anyway.
To do a factory Re-set, first press the INFO button (at the bottom left of the MFD2)
Then press SYSTEM SETTINGS to open the main menu for system settings.
In the top right hand corner will be a FACTORY SET button. Pressing that resets the unit to factory default (and hopefully turns off the AUX input that you can't reach through the CD screen). According to the manual, routes, addresses and destinations that you have stored will NOT be deleted.
Thats all I can think of for now. Good luck.