The reason it sounded stupid in the movie is because it was the name of the actual element that they were mining. The historical use of the word that you mention is for hypothetical things, e.g. in thought experiments. From Wikipedia:
"In engineering, fiction, and thought experiments, unobtainium is any fictional, extremely rare, costly, or impossible material, or (less commonly) device needed to fulfill a given design for a given application. The properties of any particular unobtainium depend on the intended use. For example, a pulley made of unobtainium might be massless and frictionless; however, if used in a nuclear rocket, unobtainium would be light, strong at high temperatures, and resistant to radiation damage. The concept of unobtainium is often applied flippantly or humorously."
I took it to mean that the geek character in the movie was deliberately dumbing things down for the person he was explaining to, out of disdain for their position. He was basically saying, "This is the most valuable substance in the universe, and we can only get it here" in as bluntly and impossible-to-misunderstand way as he could.
It wasn't in the context of "Quick, pass me that bar of unobtanium!", or other in-universe common-usage (a la "midichlorians"), but rather a deliberate simplification. ("What do we mine here? __important shit__! Now leave me alone and go back to your useless sociology experiment while I do something important!")
"In engineering, fiction, and thought experiments, unobtainium is any fictional, extremely rare, costly, or impossible material, or (less commonly) device needed to fulfill a given design for a given application. The properties of any particular unobtainium depend on the intended use. For example, a pulley made of unobtainium might be massless and frictionless; however, if used in a nuclear rocket, unobtainium would be light, strong at high temperatures, and resistant to radiation damage. The concept of unobtainium is often applied flippantly or humorously."
http://en.wikipedia.org/wiki/Unobtainium