I was raised in a society in which phrases like "oh my god" and "bless you" (offered to someone who's just sneezed) are common, so I grew up using them. Now that I'm an "out" atheist, though, they make me uncomfortable even if they are just figures of speech. I know perfectly well that using an expression like "holy cow" doesn't imply the existence of a blessed bovine, but I still prefer not to perpetuate religious or superstitious language.
There are some unwanted behaviors that, given sufficient willpower (or maybe it should be called "won't power"), we can simply decide to stop. If you dislike the effects of a bad habit such as biting your nails, you can quit doing it. That's the route I decided to take with saying "bless you" to someone who's just sneezed. If the sneeze appears to be a one-time event, I ignore it, just as I would ignore a burp or a loudly rumbling stomach or...other...bodily noises. If the sneezing continues, I offer a tissue and ask if there's anything I can do to help (like removing a flower arrangement that might be triggering allergies).
Sometimes it's difficult to simply stop a behavior, though; an acceptable alternative must be found to replace it. When I'm shocked or surprised, for example, I generally say something. I'd prefer it not be something of the "oh god" variety, but finding a substitute phrase and teaching myself to use it has been a challenge. For the moment, I've settled on "oh my word" as my new "emergency phrase."† It's appropriate for a writer, and nobody's likely to object to it. (If somebody happens to mishear it as "oh my lord," that's their problem.)
I'm making progress in training myself to say "oh my word" instead of "oh my god," but quite often one part of my brain wants to revert to the old habit while another part knows better, so I find myself stopping after saying just "Oh, my..." I hope George Takei hasn't trademarked that phrase!
† This is an occasion on which the original definition of the word "ejaculation"—"an abrupt, exclamatory utterance"—would come in handy, but English (like all living languages) evolves, and that word has a wholly different meaning for most people now.