No, nobody ever (seriously) suggested to Salena Zito that anyone objected to people saying "God bless you" after a sneeze. This is backwards 'B' carving territory.
I spend all of my social time with godless heathen atheists and probably all of them say "bless you" and some of them (probably? I wouldn't even notice because...I wouldn't even notice) say "God bless you" and more to the point no one would notice if anybody else brought the Inquisition into the room by uttering the phrase. It's just one of those "polite" things that we do because we do them. (And, no, the root of this particular tradition doesn't matter. We say these things because we were brought up saying these things.)
Manufactured stories of conservatives being victimized by liberals is a weird genre. I guess the religion angle (really, it has nothing to do with religion) gives it some extra kick over the usual "liberals are mean to me at the dinner parties they always invite me to" stories. You know these stories are not true because we are liberals and we know that liberals do not actually see the world the way that conservatives think they do. Liberals would not say the words they put into our mouths in these tales of conservative martyrdom.