A method of making a heat treated (HT) or heat treatable coated article. A method of making a coated article includes a step of heat treating a glass substrate coated with at least layer of or including carbon (e.g., diamond-like carbon (DLC)) and an overlying protective film thereon. In certain example embodiments, the protective film may be of or include both (a) an oxygen blocking or barrier layer, and (b) a release layer of or including zinc oxide. Treating the zinc oxide inclusive release layer with plasma including oxygen (e.g., via ion beam treatment) improves thermal stability and/or quality of the product. Following and/or during heat treatment (e.g., thermal tempering, or the like) the protective film may be entirely or partially removed.