There is a script + binary in the Ubuntu package which basically set up the the Ubuntu environment inside of a working Android installation.
The Ubuntu folder structure can be found in /data/ubuntu/.
Booting up is just like on every Android ROM, except the mentioned script gets started and the Ubuntu environment is getting started up.
The first proof of concept would be:
Backup every Ubuntu Touch specific file that got installed to /system to the PC, like the chroot scripts and other stuff
Flash CM back to the device
Copy specific files back to /system
By flashing either the boot.img of CM or Ubuntu Touch the desired system should boot up.
Thanks for your help!