Did I mess up my soup?!?

The flour in your recipe is used as a thickener. The reason it has you add it before the stock is first to cook off the pasty flour taste, and second, so you have a chance to easily stir out the lumps. The longer you cook the flour before adding the stock, the darker it gets, and that would make your soup a darker color as well. One TB of flour isn't really going to have much of an effect on the soup in the end though. Your method of mixing the flour with the stock and then adding it removed the possibility of lumps.