Red: It is definitely a flag used by the Missouri State Guard. The Guard used a variety of flags during its existence, including several that bore the Missouri seal that were of different colors and patterns that that ordered by General Price. There were also several varients of the Confederate 1st National used, although the number of stars differed from flag to flag. Glenn Dedmondt's book on Missouri flags includes several drawings of the various flags used during the relatively short perioid of time that the Guard existed as a separate entity from the Confederate units.

As for what was used by the state before the war, your guess is as good as mine. Some pre-war militia units carried flags with the Missouri seal on them, especially the ones from St. Louis. Whether the state used something similar at the capital, etc., is simply unknown to my knowledge.

I highly recommend Dedmondt's book.