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I would send a thank you card to the realtor with a giftcard to go out to dinner with a guest. That shouldn't be too much and go along way with them.
What kind of builder are you using? Is it a big builder where you put down a couple of thousand dollars and they build it and then you secure the loan and such or a builder where you first have a construction loan that gets converted to a residental loan?
If it is a the latter I would go with the realtor. If it is the previous as it is in my area of these cookie cutter neighborhoods I would go with the small deposit (it was refundable with the builder we where going to go with) and you don't have to close until everything is done and you like the work.