“Polite comeback” sounds like an oxymoron.

I would tell them: Christ needs your worship. Let him come to you. You have the power.

I wouldn't be interested in a comeback. I'd try to change the subject...

I don't understand the question.

Nope they have to realize that themselves

Could you please pass the sugar” or “did you make these biscuits yourself?”

How about I'm struggling really hard to find intelligent life among the followers of religions.

Ask if they mean "struggling with reality "

I would be unable to give a polite com back. The best I could do would be "uh-huh".

In reality, none of my friends are sufficiently religious to make such an observation.

Who?

Say "Are you also struggling to find Santa Claus again?"

I think when people are struggling is not a good time to complicate things for them by challenging their worldview. Being a good friend, being sympathetic, non-judgmental, supportive, willing to listen, etc. may be more helpful. Role-modeling is often a better teacher than lecturing.

I really don't know what say, except reality is setting in.

Welcome to asylum. Enjoy your stay.

I can't be polite with those kinds of conversations. I either have to get up and
leave, or if asked directly, give my honest position.

I can't do the whole "live and let live" thing anymore.
It doesn't work.

I'm reluctant to challenge someone when they're down and apparently seeking feedback. I would be tempted to tell them to let go of their fantasies. But, nobody has ever put themselves in that position with me.

A polite, but thoughtful response might be "Maybe they aren't actually struggling. Maybe they're very comfortable with where they are now."

This subtly shifts the focus away from god, and toward the person in question. It (hopefully) redirects their energies toward wondering, rather than judging.