I am confused as to what check and balance there is to the judiciary if they choose to violate the Public Use clause of the Fifth Amendment?
Congress has the power of the purse and can and has used funding to voice its dissent with the Executive Branch. Why is this a problem when applied to the Judiciary? If there are true checks and balances, the Court isn't exempt from an act of Congress any more than a President is.
Your question is a perfectly good one. Congress has the power of the purse and withhold funds, it's in Article I.