Well, I think that if Siegel and Shuster only referred to religion when they gave an important villain a name that might refer to Martin Luther, then that doesn't mark them as religious in my book. If anything, it suggests to me that they did not much like religion.
For me, a symbolic condemning of religion (specifics or in general) is bringing religious content into a story. Bringing it in in negative fashion, but still definitely including it.
