This is an unfortunate situation. I agree with the other posters: You do not owe her anything if you did not sign an agreement with her. She is being very aggressive, probably because the market is so slow right now.
The seller usually covers the agent's fees. The builder wants to add $5,000 to the cost of the house because they don't want to pay the commission. Do you know how the agent arrived at the $5,000 figure? Was her percentage ever discussed? Commission is not set in stone. She could come down on it if she wanted to. Perhaps you, the builder, and the agent you could all work something out so that she can still represent you, but at a lower fee (and not at your expense). With the real estate market being the way that it is, I would think that they both would be willing to compromise a bit.
Good luck -- I really hope you get your house!