Yes, you DUmasses a president IS allowed to declare a US citizen an enemy combatant, i.e. George Washington calling out federal troops against the Whiskey Rebellion. If a president is allowed to do it vs domestic tax proresters all the moreso is he allowed to do so against someone seeking to engage in unlawful acts of war against the US in the name of a foreign power.
What is the check and balance?
Simple. The president issues an order naming a specific person and a specific reason for his actions. If that order proves to be unfounded or worse malicious than the president's name is inextricably linked to that action making him susceptible to the wrath of the people and their representatives.
Get it?