I would suggest canceling the leaving developer's subscription (which I might guess you would be doing regardless), and add the paid subscription to another account. Then recreate the app(s) on the new paid account.
Transferring the paid subscription on our side isn't really an option.
I can understand where key management on a collaborated app can cause issues / confusion -- its been discussed previously, but having a shared application being associated with multiple signing keys at once causes issues of its own. But yes they an app is always built using keys set by the app owner. On iOS, all developer devices should be added to the provisioning profile.
If multiple developers need to manage the keys is certainly an option, if multiple developers need to manage keys. Alternatively each developer could maintain their own App on build, and just link to the shared source code (github?).
For the account side, its not so much sharing an app, its a case of sharing the quota. There is a quota of 25 apps, each developer would be able to create their own instance of the app from their own branch / zip upload. Currently the only way to share quota is to use collaborators, but you can't really have multiple collaborators on a single app as they would overwrite each other's changes and interfere with each other's work.
The second part is that the plan and all the apps created would belong to the organisation rather than the specific developer account so that when a developer leaves their account can be removed from the organisation. This would then remove the apps they created.
You would probably want to have a way to also create release versions associated with the organisation rather than a specific developer. This would allow each developer's instance to be associated with their developer signing keys only, and keeps the release keys separate from any specific developer.