There is provided a method of making a heat treated (HT) coated article to be used in shower door applications, window applications, or any other suitable applications where transparent coated articles are desired. The method may include heat treating a glass substrate coated with at least a layer of or including diamond-like carbon (DLC) or other type of carbon, with a protective film thereon. In certain example embodiments, the protective film may be of or include a layer of or including SnOx prior to HT. Optionally, a release layer of a material such as zinc oxide may be provided between the SnOx and the DLC. Following and/or during heat treatment the SnOx transforms into SnOy (y>x) so that stress is created due to the SnOx to SnOy transition. Then, during quenching, stress relief may occur which causes the layer to buckle, creating cracks which may act as liquid channels that permit the sacrificial film to be easily removed via washing or the like.