You know, more that I look at the Saint-Domingue expedition, it seems to me that the French ran into quite a bit of bad luck. I mean they lost their Supreme commander (Charles Leclerc) and one of the more capable generals (Antoine Richepanse) to Yellow fever, while the only Général that might have been able to reconcile the native elite to French rule (Jean Boudet) was heavily injured and forced to cede command to the Vicomte de Rochambeau, whose extremism and incompetence united the entire population against him. Not to mention Leclerc failed to properly disarm Lourverture's junior officers, even though it should have been obvious to him that only slavery was reimposed they would all defect/rise up. Then, on the flipside, the only leader the Haitians lost was Lourverture.
So, what if that situation was reversed, with the Haitains losing all or most of their leaders and the French only losing Leclerc and Rochambeau (and leaving Boudet in charge to sweeten the pot)? I mean I can easily find instances where both Jean-Jacques Dessalines and Henri Christophe could have died in the early months of the expedition, while Alexandre Pétion could have been arrested and deported with Lourverture. Maybe combine this with NOT removing André Rigaud, the most pro-French of the Haitians and the one who could have brought the mulattos over to the side of the French (provided that they're given full citizenship and are considered equal to the whites in the equality in the eyes of the law). It might be a bit hand-wavy but I think its doable. Plus it likely wouldn't effect the rest of the Napoléonic wars all that much; cash-strapped Napoléon would likely still sell Louisiana to the U.S. and, in the event of a Spanish reconquest of their half of Hispaniola, the French would just retreat back to Saint-Domingue.