The reason I brought up the confession is that Charlie was Catholic in his flashbacks. That is a facet of his make-up, how he views things, it is the part of him that is the "man of faith" (he was proud to tell Eko he had been an altar boy). Are you a man of faith or a man of science is a theme of the show, faith and science not neccessarily being strictly and formally defined. It's like Stewie said, it is a spiritual gesture, motivated, perhaps, by that religious element that is a part of Charlie's upbringing.

WHICH
would lead to an interesting endevour... who have beend declared "men of faith" and who have been declared "men of science" ~and~ can you change from one to another?
* Locke said of himself he was a man of faith
*Locke told Jack he was a man of science
*Is Doc Artz a man of science - he had all those jars of bugs?

__________________

`Dear, dear! How queer everything is to-day! And yesterday things went on just as usual. I wonder if I've been changed in the night? Let me think: was I the same when I got up this morning? I almost think I can remember feeling a little different. But if I'm not the same, the next question is, Who in the world am I? Ah, that's the great puzzle!'

-- Alice, from “Alice’s Adventure’s in Wonderland”