In a large, heavy pot or Dutch oven, cook the chopped bacon over medium-high heat until crisp, about 4 minutes. Using a slotted spoon, transfer the bacon to a paper-towel-lined plate to drain.
Place 1 cup flour in shallow dish; set aside. Add 1 tablespoon of olive oil to the bacon drippings in the pot. Sprinkle the chicken thighs with salt and pepper. Working in batches, coat the chicken thighs with flour and add to the pot; sear until brown, about 4 minutes per side. Arrange the chicken thighs in 15x10x2-inch glass baking dish (or any combination of glass dishes that will fit the chicken).
Spoon out all but 3 tablespoons of fat from the pot. Add the shallots and garlic to the pot and sauté for 1 minute. Add the onions, crimini mushrooms, and marjoram and sauté until onions begin to brown, about 10 minutes. Add the red Zinfandel and bring to a boil, scraping up the browned bits. Add the chicken stock and bacon; boil for 5 minutes.
Pour the wine mixture over the chicken in the baking dish. Cover tightly with foil; bake until the chicken is cooked through, about 1 hour.
Using tongs, transfer the chicken thighs to the platter or a large, deep bowl. Strain the wine mixture from the baking dish into a heavy medium saucepan. Transfer the onion and mushroom mixture to the platter with the chicken; tent with foil to keep warm. Mix the remaining 2 tablespoons of flour and butter in a small bowl to blend. Bring the wine mixture to boil. Whisk in the flour mixture and boil until the sauce thickens and is reduced to 2¾ cups, about 8 minutes. Season the sauce to taste with salt and pepper.
Ladle the sauce over the chicken and vegetables; sprinkle with chives.