Those were my first thoughts, confirmed by a bit of investigation, starting w/ the primary source.  This analysis by a biology doctoral student concurs.  We shouldn't have to do this kind of research to get the truth behind the studies - the journalist should.  Instead, we get hype, since hype gets ratings.

Germophobia is dangerous for many reasons.  We should also know that all produce has bacteria and yeasts that come from the air and are present before it is even picked.  That's what the traditional food storage method of lacto-fermentation counts on for its success.  Those bacteria are almost exclusively beneficial, and populate our gut to form the bulk of our immune system.  We even take them in capsules - "probiotics."  The beneficial bacteria are present on the lemons to make us healthier, and the pathogenic ones are not pathogenic in such small, naturally occurring, amounts.

If I were really concerned about restaurant lemons, I think I'd be sure to skip the sugar, get more D via the sun, and eat plenty of probiotics at home that week, too.  ;)