usually the file transfer is a p2p process so the server has nothing to do with it. But the packets to initiate a filetransfer are transfered using the server. As far as I know the commercial Wildfire EIM allows to block file transfers but not to capture the files so far.
I could imagine that Matt will add support to do this by simply modifying the “initiate filetransfer” packets that the clients talk to the server instead p2p. While the server simulates two clients, like a man-in-the-middle attack.