Maybe I'm missing something, but even with geolocation and all sorts of tricks this will never be working 100% "safe". Not even if you had two completely separate websites, and sure not if it were two sections of the same site. With several factors in the game called Internet, there are always ways how a European visitor could see your USD section, intentionally or accidentally. Sorry.
But to answer your immediate question: out of the box you can install only one shop in one Joomla instance. There are ways (= extensions) which enable you to "combine" two or even more Joomla instances on the same server, even incl databases, user accounts etc, plus the mentioned geolocation to route - some (!) - users to the "right" section, but then again, there will still be visitors making it into the "wrong" store.