Actually it is trivial to use a normal pixel graphic file to hexes with the normal 1 pixel = 1 tile.
All you need to understand it that every other row (or every other column, depending on which way the hexes are turned) will get shifted over half a tile-width.
See attached image. Yes those aren't exactly hexes in the bottom map-- i left them as squares because it was less work, and it's more obvious that i haven't pulled a bait and switch. Notice that each tile in the bottom map is surrounded by 6 others. You don't have to imagine very hard to see these as hexes.
Granted things get shifted around a little, but you can clean up any issues in Civ V-- assuming there will indeed be a way to import pixel images as the basis of maps
