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That is one thing you could do. You could also try it with ImageMagick. I scan with a multifunction machine which sometimes do this. Only, that machine gives me a pdf and for pdf I can use pdftk to do that easily.
If ImageMagick can't do it in one step, you might want to convert the images to pdf (with ImageMagick), combine all pdf's into one (with pdftk), rotate every other page (with pdftk), split the pdf into separate pdf per page (with pdftk), convert the pdf's back to images (with ImageMagick). Quite a route...
You might also try a program like XnView or IrfanView or something like that. There you can select multiple images and rotate them.
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