Buying minifigure parts at the Lego Store
Short Answer: Yes, you could buy minifig heads at a lego store. 
Caveats: The heads are part of the "build-a-mini" feature of the lego store. So while you could technically just pick 1 head, you would still be charged for the whole set ($9.99 in USA, I believe). So you may as well pick whole minifigs + 1 accessory + hair/hat. Variety of head, torso, legs and accessories is limited and poor...

If you're ok with "generic", then it may not be so bad. If you need to build an army of medieval hun knights stormtrooper with galactic helmets... not so much.