I agree about the preference for cooking separately, but if you've ever had braised duck in a really good Chinese restaurant, you'd find that it can be fantastic. And it seems like sous vide would be perfect for this dish.
I don't have a recipe handy for Chinese braised duck (you can Google one), but sous vide for 8hrs at 170 should give you great results. I would consider removing the skin to eliminate excess fat, else you can skim after. And cut duck in half for better heat transfer. Add recipe ingredients, seal and go!
If you don't want to head the Chinese route, "Provencal style" with tomatoes and herbs could be great, or cook with a little onion, garlic and bay leaf, then shred and add to mole sauce for enchiladas or use in tacos.