That leaves the final option: The president could claim the inherent constitutional authority to revoke the clearance eligibility of each of the individuals without any due process. There is no precedent for such an action, as no president (at least as far as I am aware) has ever personally intervened in the clearance revocation (or approval) of an individual. That has never happened before because past presidents—whatever their flaws or scandals—knew there were certain institutional norms and customs that a president simply should not disturb.
Trump, though, is not burdened with an affinity for respecting institutional norms. He already bulldozed those norms when it came to hiring his daughter and son-in-law, refusing to place his assets in a blind trust, and refusing to disclose his tax returns. What is to stop him from running over another norm?
If the president were to take this unprecedented exercise of his authority, it is anyone’s guess how the courts would construe the issue. It would set up a serious clash of constitutional questions between the inherent authority of the president regarding classified information, the procedural due-process rights of clearance holders under the Fifth Amendment, and the extent to which the judiciary is even permitted to rule on the matter.