Since the Iodine ideally gets absorbed into the bloodstream within the first few inches of small intestine, to be used in strengthening the epithelium across the body against bacterial and parasitic invasion, my instinct is to say no, it's not harmful to beneficial bacteria.
It is, however, used to kill parasites! It strengthens the ability of cells to create hydrogen peroxide, one of the body's defenses against infection.
The first few inches of small intestine are meant to be primarily sterile anyways, since that is where bile is mixed with chime from the stomach to continue the digestion of food.