Trump should make the clearance people give them a real reason for not giving a clearance, and if it does not make sense he should order the clearance. The President can give clearances to whoever he wishes. The swamp can stall and deny a clearance for any reason, unless the president overrides them.
Heck -- the whole thing became a joke when President Trump named this 36 year-old neophyte with no experience at any level of government as a "senior advisor" in the White House.