Seems pretty obvious that there will be something to make her go back to McCullen and the Commander, as you can't have a COBRA without The Baroness. It'll be her struggle, and the source of most of Duke and Destro's drama, most likely.
And also:
In "The Mission That Never Was", it is revealed that the core G.I. Joe members were sent on one final mission, which resulted in Cobra's Brainwave Scanner being corrupted by a virus that spread through the entirety of their mainframe. Crippled and defeated, Cobra then fell to a "unified military attack" (this attack is never detailed in a story, but hinted at in various "Battle Files" entries). A happy side effect of this confluence of events was the incapacitation of the Brainwave Scanner. Without repeated "self-medication" via the Scanner, the Baroness was freed from her artificial loyalty to Cobra
It would appear that angle has been explored in the comics as well.