There is no Joseph listed with the Jaeger family, at St. Jude Cemetery.
Many of us here have kin that fought on both sides of the war. Nor was it unreasonable for them to switch sides. There was an awful lot of cruelty committed by both sides and I would presume that this would be the reason for the switching back and forth...
As far as the EMM:
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Mandatory Enrollment Date in New Enrolled Missouri Militia
Location: Statewide
Date: early August 1862
Sources: newspaper "Daily Missouri Democrat" of 4 August 1862 and Hamilton, "The EMM," "Missouri Historical Review," July 1975, pp. 417-9
Description: The mandatory enrollment of all able-bodied MO men age 18 to 45 across the state to begin MO's emergency home guard army called Enrolled Missouri Militia created uproar across the state. Hundreds of new men across northeast MO rushed to join Rebel COL Joseph C. Porter's Rebel recruiting command and elsewhere others joined either southern recruiters or guerrilla bands. Many men left the state and hundreds hid out in the countryside to escape having to go to county seats and enroll in the northern militia. Tens of thousands of Missouri men did enroll as ordered including a number of Monroe County men into the 70th Enrolled Missouri Militia Regiment. Missouri Union officials, worried by both the presence in the state of dozens of Rebel recruiters and guerrilla bands and the removal of many Union troops to hotter war fronts, were able to field a cheap, untrained army capable of little else than self-defense. This amateur army of seventy-some-odd regiments managed to assist the few remaining regular Yankee troops in defending the state against Rebel onslaught throughout the rest of the war.
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Otherwise, I know nothing of Joseph. Should I discover anything new, I will respond accordingly.