I did some thinking about this, and I think they should leave the floor as is, and use the money that would have been used to remove it, to make an interactive educational tool to explain the differences between the two. There can be different aspects in the exhibit. People who experience will learn geography (all parts of the world that used this symbol), Arts & Crafts, American History (Native Americans), World History (the change of the symbol by Hitler), and hopefully with all that they will come away knowing what happened in WWII Germany, and why it "never again" is so important. By educating people it removes the hateful associations, and therefore the power is returned to those cultures that are being punished for Hitler changing it for his evil purposes. A similar turn around has been done with the gay community and the pink triangle. The pink triangle was used in Nazi Germany to identify sexual deviants, and is now a symbol that was used in the gay rights movement.
I also think, that removing symbols of other cultures, specifically Native North American cultures, is bigger problem. It may just be a floor in the Bonneville County Courthouse, but the symbol is in many other places. Should the Capitol Building in DC be next, or the Philadelphia Museum of Art? The article below mentions that historical pieces of these people are hidden away because of Hitler, and they stopped using that design because of him. Why keep letting his hate oppress the history and culture of people that lived here for thousands of years?
http://www.collectorsguide.com/fa/fa086.shtml