I say that there is no problem as long as the "unorganized militia" consisting of an armed citizenry is prepared to protect their own security.
The fathers, mothers, brothers, sisters, and neighbors of the federalized, organized militia will be prepared to respond with their own weapons to any threat to their freedoms. The federalized, organized militia will find themselves asked to act against the best interests of their families and many will not do so. Such a standing army cannot rule an armed citizenry.
The state militias were not under federal control. An act of Congress could call forth the Militia "to execute the Laws of the Union, suppress Insurrections, and repel invasions" only.
Other than that, they were under state control.