I'm hoping you procured representation on this rather than going through the builder representative to act on your behalf.
If the floors were installed at your request you would be responsible for the cost. If you made the offer after they were installed OR the builder installed them in error then it would be their issue. But if they are offering to let you have that very expensive upgrade remain for just a portion of the cost it might be reasonable to work with them. Depending on the builder they might rip them up out of spite. Hardwood is going to be a much better investment in the long run for your homes value if it fits your lifestyle and taste.
Did your offer include hardwood floors? Have you read over the portion of your contract that pertains to what the builder includes and any "upgrades"? Did you consult with the builder representative as to what was standard in the property for the price you were willing to pay verses what was an upgrade? These are important questions and ones that normally a Realtor will ask verses a home buyer without representation. Please consult your contract and if you do not have any buyer representation then get yourself a good real estate attorney--you'll need one.
All the Best!
You have to make sure you understand exactly what the builder is offering and what the conditions are when you're buying new construction. If you didn't use the representation of a real estate agent, now might be the time to get counsel to help you maneuver through this if you are still concerned about this issue. If the builder upgraded the floor and you didn't ask for it, then I see counsel being your best option to solve this dispute if you all can't come to an agreement.