I have some interior walls in a plan as different layer and need to turn them off for a proposed plan.
Is there a way to have the walls heal when I turn that layer off so it does not leave gaps in the walls?
(see yellow arrows in screenshot attached.) What options do I have to make it work?
Turning a Wall's layer off (or freezing it) will not prevent Wall Cleanup, as you have discovered. The only solution I can think of would be to put the interior Walls into a separate Wall Cleanup Group. But then they will not cleanup with the other Walls at any time, whether on/thawed or off/frozen. Only you can decide if that is a problem.