Hi exonerated, I will not have access to my Raspberry until Monday, so it will be difficult to me to do some tests. Anyway I will try to help. I don’t know if having a PS3 controller synced should be a problem, but it can be.
What I can see from your commands is that the BT MAC that you are using to delete the PS3 controller is the BT USB dongle MAC, not the controller MAC, that must be the problem. When you run hciconfig you can see the proprieties of the BT USB interface, it is needed to know only the number of the device, in your case it is “hci0”, the MAC that is displayed there is the dongle MAC, not the PS3 controller MAC that you may need to remove.
If you have your PS3 controller with you, you can get its MAC doing the “hcitools scan” command and by put the controller in paring mode. That’s the MAC you have use in the bluez-simple-agent command.
If that doesn’t work, it could be better if you try on a clean RetroPie to avoid any sort of problems. ;)