I see. That is the beauty of how collabs works. It simply puts up dividers to create spaces and enforce permissions. It doesnt have to imitate or recreate the functionality of an app to work. Thats how it is so flexible to work with nearly any new content app release that follows IPS conventions out of the box.
You disabling the app is like taking the dividers down.
When you uninstall the app, you can choose to have all content inside of collabs removed as well. If you dont, you are left with them.
I dont see any more ideal way it would work.