Can this be fixed in a system where commanders are created anew?
One change (not a direct fix) could probably be making commanders unable to cloak while morphing. Though the question remains whether this is wanted.
Another fix could potentially be a new commander system I read about. If morphing a commander did not create a new unit but rather change an existing unit (which would be possible, but not without some limitations) then bugs like these would not occur. From what I understood some people are already working on this. As such, a direct fix to the issue would not be needed in the long term, provided that the new system gets accepted.