I imagine the atheist would just say "bless you" Also I don't know why this is apparently so controversial. Language has theistic underpinnings, but I think atheists can acknowledge that without being offended every time. After all, if we don't need to purge Thursday from the week then maybe we can tell people "bless you"

No but it's offensive when someone who's not religious wears a cross necklace.

is this a serious question