What source have you seen this in?
It's very different from what I've seen which is that Sec State Madison held Jefferson's feet to the fire to support the slaves and that is why Napoleon surrendered Louisiana -to get us to stop supporting them so France could have her rich plantations back.
Before his presidency Jefferson did advocate crushing those rebel slaves.
Try The Presidency of Thomas Jefferson by Forrest MacDonald.
Jefferson's very first act as president was to order Madison to impose an embargo on trade with the Haitians and try and starve them into surrender.
Adams had established diplomatic relations with the rebels and Jefferson put a stop to that immediately. He in no way supported the slaves and the entire South was terrified over this development. So much so that any news from the island was repressed. Papers were not allowed to publish information about it and ships from the region were carefully controlled to prevent spread of such news.