He was still the properly elected governor though, and while he favored secession, the legislature had voted him down on that issue, thus Missouri was still in the union. When all the votes were taken, Missouri wanted to remain neutral and avoid the war itself. But Lincoln marched his army in, and when the state government protested that army's invasion of their neutrality, the army went after the state government. In short, Lincoln invaded, conquered, and removed the government of a state that, at the time this act occurred, was still in the union and had even expressed a desire to stay in the union and out of the war.
I guess you have no comment on the rebel invasion of Kentucky.
Too, Lincoln didnt have to send his "army" to Missouri. Local federal authorities and loyal Union men there were able and active.
Walt