Would they really make Davis General of the CS Army over Robert E. Lee? If so, would Lee have a change of heart and join the Union forces?
Lee was never "General of the CS Army"=to General In Chief USA. OTL the CSA never had an over all commander of all armies other than the Davis as President. What I am speaking of is Davis having a position similar to Scott, McClellan, Hallack, and Grant did in the union. In the CS Army it was the president then army commanders like Lee, Bragg, ect.. Occasionally the CSA did have Theater Commanders to on paper were over a whole Operations area ie. J.E. Johnston in 1863 in the Western theater.
At the start of the war Lee was the commander of the Virginia Armed Forces ie the Virginia Militia and then commanded forces in Western Virginia (West Va today). Then he was in charge of Coastal Defenses in Savannah Ga. Before becoming Pres. Davis Military Adviser in 1862, and finally head of the Army of Northern Virginia after Johnston's wounding at Seven Pines.
So no this wont stop Lee from siding with Va. it might mean that he becomes a Corps commander under Davis. or even scarier for Lee ends up like Meade in 1864 the technical commander of the Army of Northern Va but with Davis riding along telling him what to do.