The only way that I could find to convert a Sony cam MXF file was to use MXFSplit to pull out the raw stream and then use FFMpeg to convert that to something.
Step 2:Drop to a command line, CD to the directory containing the files from above and run the following command on your file:
Step 3: The previous command will give you a *.Stream file which is a raw DV stream that we can pass to FFMPeg:
ffmpeg -y -i "
.Stream" -s 640x480 Output.mov