According to the Militia Act of May 2, 1792, as amended Feb 28, 1795, Sec. 2:
"And it be further enacted, That whenever the laws of the United States shall be opposed or the execution thereof obstructed, in any state, by combinations too powerful to be suppressed by the ordinary course of judicial proceedings, or by the powers vested in the marshals by this act, it shall be lawful for the President of the United States to call forth the militia of such state to suppress such combinations, and to cause the laws to be duly executed. And if the militia of a state, where such combinations may happen, shall refuse, or be insufficient to suppress the same, it shall be lawful for the President, if the legislatures of the United States be not in session, to call forth and employ such numbers of the militia of any other state or states most convenient thereto, as may be necessary, and the use of militia, so to be called forth, may be continued, if necessary, until the expiration of thirty days after the commencement of the ensuing session."
You'll note it says nothing about a state having passed an ordinance of secession to be a bar to federal action.
The Judiciary Act of 1789 requires that "controversies of a civil nature" between the states be submitted to the Supreme Court.
Maybe secession was a criminal controversy?
Walt