PDFLRF does similar jobs as Rasterfarian and it can save the result as zipped PNG files.
If you find a way to convert a set of PNG files into one mobipocket file, using PDFLRF might solve your problem.
PDFLRF can cut the PDF pages to fit 6 inch sony reader screen either in landscape or portrait mode. I don't think you can cut the screen in half exactly, though. I would recommend you to try the program and how it performs.