“was so unusual that it raised a “plausible question” about the legitimacy of the move”
in other words,
Sullivan views the current Justice Department as illegitimate.
For him the Obama Justice Department remains the legitimate Justice Department.
When Sullivan raises the specter of the legitimacy of the DOJ dropping charges (i.e. Trump made them) what he’s really saying is that he wants to expand his persecution of Flynn and put the President on trial for abuse of power.