I don't think Marlborough joining the Jacobite cause was particularly likely. Churchill had been one of James' top men for years, even while he was Duke of York, so there was already an enormous connection between them, but it was in this role that Churchill "earned" his earldom by his machinations in turning the English Army - including a great number of James' other loyalists appointed to places on his taking the throne - and bringing them wholesale with Princess Anne in the mass defection to the Dutch invasion force in 1688.
Marlborough effectively made his decision there; at best, James "III" simply couldn't trust him with anything important because of his very, very intimate treason, and at worst, would simply want him dead. Even if Marlborough changed his mind, it would have probably been impossible for him to work actively with or for the Jacobite court, despite his connections there.
Further, if you look to the specific point of contention that led to his split with the Queen, it just isn't possible. The Duke publicly sided with the Whigs in Parliament against the Tory peace plan in 1711 for the express reason that it would be a betrayal to Great Britain's allies on the continent - and Marlborough did explicitly name Prince-Elector George, the heir apparent to the heiress presumptive, and his strong opposition to Great Britain pulling out of the war. The Queen going along with the Tories, and in a speech calling out Marlborough for effectively being too loyal to the Hanoverians, makes it somewhat outside his own motivation to suddenly go over to the Jacobites.