I have not worked in the retail setting for some time but this was one of the reasons I don't. It can be pretty lonely when you're the only one there at 0300 in "sporting" areas.
That's one of the pluses to being a pharmacist at a big box store (as in Walmart, Target, grocery stores, etc., not the neighborhood small convenience pharmacies). They're a harder target for robbery; not that they won't get robbed, but that you simply can't and won't get all the witnesses. If you shoot somebody (be it the pharmacist or a tech), there's a large number of other folks in the store who are potential witnesses that you cannot get. Furthermore, the pharmacy may be a bit of a hike from the door (not always, but sometimes)... that means there's no such thing as a quick getaway.
It forces a bit more introspection on the part of the criminal, and as always when dealing with criminals, the harder the nut you are to crack, the more likely they'll go find an easier mark.
I'm not saying that companies are right in this kind of policy, I'm just saying that there's more to this equation than just giving the pharmacist a weapon.