Over the last several weeks I have been in touch with a number of concerned Bosnian citizens and experts who helped draft the UNESCO letter. There is clearly international concern here, and many Bosnians are fearful that Mr. Osmanagic's team is destroying Bosnian cultural history in an effort to prove a preconceived idea, rather than test the idea against evidence gathered with professional integrity.
I signed the letter largely to protest the fact that Mr. Osmanagic has no professional qualifications and should not be directing scientific excavations. As a professional in historic preservation I also share the concern of my Bosnian and other European colleagues who legitimately fear for the loss of important archaeological data: 1) because Osmanagic is not a professional and probably overlooks far more than he catalogs simply because he lacks professional training and experience in archaeology, and 2) like most amateurs out to prove something, he's undoubtedly destroying evidence that doesn't support his view.
Archaeology is as much an art as a science, and archaeologists are keenly aware just how many priceless historical artifacts have been damaged or destroyed by amateurs with an agenda. They are right to worry: axe-grinding amateurs can and have destroyed irreplacable historical sites.
Wikipedia has more information on the Bosnian pyramid. It details how Osmanagic has already lied about the work going on at the pyramid, the data found, and the involvement of other archaeologists.