There were a few who did just this, however; there was at least one RA officer who fought at 1st Bull Run with the U.S. Forces and then, essentially, deserted and ended up with rebels, and quite a few former rebels who took the oath and became "galvanized." Interesting example is EW Gantt, who commanded a rebel regiment from Arkansas, surrendered with McCown's force at Island Number 10, and then declared for the U.S.
I don't think that is really possible here. Lee isn't just another officer. ATL, he is THE face of Unionism. He started the war even before Lincoln took office! Lee's face is being illuminated in torchlight recruiting parades from Minnesota to Maine. He is certainly being denounced as a traitor in Confederate newspapers and by Confederate politicians from Richmond to New Orleans.
Especially given Lee burning the supplies on a technicality. Confederate press and political opinion was not given to nuance or even to fair analysis of the facts Which means that Lee has probably been publicly denounced as a scoundrel and a cheat, including by prominent Virginia figures and newspapers. In fact, there's a reasonable chance that the Virginia secession convention passes a resolution denouncing him. Under those circumstances, the South wouldn't have him and there is no chance in hell that he would offer, because his dander would be up. When Lee got his dander up, look out!
As if that weren't enough, there is the fact that his exposure to the Confederacy is Ben McCulloch and his gambling, drinking rowdies. Lee now sees the Confederacy through the lens of blackguards and ruffians. Who don't understand honor or obey the law (Lee is clear in his mind that McCulloch acted before secession actually had been legally enacted and is also clear in his mind that absent a declaration of war, a seceded Texas had no right to attack his command).
As a final factor, remember that Lee is loyal to his officers and soldiers almost to a fault. ATL, Lee seems to have already developed a special relationship to the rock-solid Union-loyal Thomas, so that's going to draw him.
Basically, given the events described in 'Lee at the Alamo,' I see very, very little chance that Lee would ever consider taking a Confederate commission and very little chance that one would ever be offered to him.
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