I take most things from TOS with a grain of salt as I find they don't always translate to the rest of the series anyhow. Religion certainly still exists all over the place throughout Star Trek though, so it's not completely ridiculous to think that Kirk still holds some vestiges of a monotheistic religion. Habits can be hard to break, case in point is the colloquialism that you used to end your question.

It was the same way, all too often, in classic Twilight Zone episodes. The heavy-handed insistence on the heaven and hell dichotomy and the need for infinite punishment for finite crimes weakened the premise.

Equally disturbing was the episode where they are commenting on aliens whose society is basically native American. Spock makes a comment about them worshipping the sun, and Kirk replies not the "sun" the "Son."