Hello Bethie and thanks for your post.
As Robin noted below, as of July 1, 2009, the institution of a new law called the Home Valuation Code of Conduct (or HVCC) requires a third party called an Appraisal Management Company (or AMC or AMS) to be the only contact that may assign an appraisal job to an appraiser. The intent of the laws (which affect Fannie and Freddie loans) is to remove anyone with an "interest" in the loan from being able to influence the price of the home. These new procedures have, in many cases, resulted in some very low and questionnable appraisals due to the unfamiliarity of the appraiser to the general area and there are many stories even here on Trulia regarding problems in selling or financing homes as a result of the new HVCC rules. However, the very thing you are worried about (that the mortgage broker and buyer somehow manipulated the appraisal) can no longer happen under the new laws.
Regarding your second question about relationships, a loan officer and a buyer will, in many cases, have preexisting relationships. When you are trying to buy something as big as a home, it is often more comfortable to work with a friend than a stranger--this holds true both for Realtors as well as loan officers and mortgage brokers, and there is no reason that the relationship must be disclosed. Even without the HVCC, such relationships were not considered noteworthy of disclosure. So, unfortunately, there is no agency that will handle this complaint at this time.
Finally, as to your options, speak with your Realtor, but you do have at least two options that you might wish to explore: 1) Hire your own appraiser and get your own appraisal. If the buyer chooses not to get a second appraisal, your own appraisal might refute the price or provide additional information that the lender might reconsider; and/or 2) choose not to sell your home to this buyer. Unless your contract specifically requires you, as the seller, to reset your price to the appraised price, there is no imperative that forces you to take a financial "bath" on the home if you feel that such a loss would be unwarranted or unaffordable at this time. Again, speak with your Realtor about the pros and cons of any decision for your home.
Grace Morioka, SRES, e-Pro
Area Pro Realty
Web Reference: http://gracemorioka.areaprorealty.com