In Galileo Seven Spock also says something like, "I, for one, do not believe in angels," indicating his skepticism about an afterlife. Does that make Spock the first (implicitly) atheistic character on a network TV series?
Beats me. I'd guess Twilight Zone, Outer Limits, Dr. Who or some other show snuck the concept in somewhere.
Hopefully at least one or two would show a virtue of non-straw rationality.
Episode list