Like nature, time comes up as a theme in "Church Going" mostly for the purpose of showing how temporary humanity's time on earth actually is. In fact, Larkin's speaker suggests that it's because our time is so limited that we have a longing for some higher purpose, or for some sense that our lives will still be meaningful after we're gone. For this reason, we might believe we have immortal souls that'll go to heaven. Or maybe we believe that our time on Earth is best spent by treating others with compassion and kindness. In any case, the fact remains that all human beings will one day die (deal with it, people), and the inevitable passing of time is deeply connected to humanity's urge for spiritual significance.
According to "Church Going," time is the one thing that even a skeptic can't question. It's just a brute fact of existence. (Don't believe us? Try arguing with your boss about the abstract nature of time the next time you're an hour late to work.)
In "Church Going," the passing of time is a cause for celebration (break out those clock-themed party hats!), since it clears away old nonsense and replaces it with new and better things.