Esten Cooke was not second in command.He was for a brief time (90 days, I think) an aide, writing letters etc.Gen. Stuart did not particularly like him.
Before the war the Cookes were close to all three of their daughters and husbands.Stuart was posted to the Kansas/Missouri area, and so was Col. Cooke.
Stuart believed, apparently from family conversations, that Col. Cooke would resign an enlist with the CSA, since he was a Virginian.Stuart didn't know until the fact that Cooke was going to fight for the federals.
Stuart was angry and emotional and he and his wife, Flora, cut off the Cookes.Flora did reconcile with her parents in the years after the war, but apparently did so with mixed emotions, since her husband had died for the Confederate cause.