A getaway is merely a vacation of a few days. Perhaps three or four days. A commissary is grocery store on a military installation. The Pentagon is a military installation.

When we need a vacation, we often say that we need to get away from it all (the work, the stress, etc.) and relax. So, such vacations, particularly if they are short and planned quickly, are often called a "getaway." Usually, they are in a particularly relaxing place, like a resort island. In an office building, there might be a cafeteria for the workers to have lunch. That cafeteria, particularly in a government office building, may be called the "commissary." But not always, usually it's just the cafeteria. In the movie, I think Young Tony is making a joke implying that they are going to wind up getting stuck at the Pentagon, and so their "getaway" is going to be at the Pentagon's commissary, not the Bahamas. (although I have not seen that particular Ironman movie, so I'm not sure.)