Remove all operational controls  from said employee/executive, while allowing them to keep their title and/or /Civil Service GS rating until they can be removed by the proper procedures.  Something tells me that even a 100K+ salary and an office of their own would hold little attraction to the "burrowed in" operatives if it became clear they had no operative responsibilities.

If they whine and complain about how they have been marginalized, give them an important title and the ability to write reports about something really unimportant.

It would be a (temporary) waste of money, but it would remove an obstacle from achieving Obama's policy goals.