Just looked at the source code. There's an option to disable cropping via command line. It's just not available in GUI. I don't have access to a 64-bit PC right now (using the precompiled binaries) so I'll just have to check it out later.
Code:
processingOptions.add_option("-c", "--cropping", type="int", dest="cropping", default="2",
help="Set cropping mode. 0: Disabled 1: Margins 2: Margins + page numbers [Default=2]")