@kurbitur I think imagemagick?
random starting point: http://www.imagemagick.org/discourse-server/viewtopic.php?t=28386
"If you want to work on a separated image you need to be intimately familiar with the way CMYK images work. If you look at Gimp's Layers window after separating an image, you will witness the ingenious way in which the separation is done. However, editing the image is not as simple as with proprietary software like Adobe's Photoshop. "
@kurbitur did you tried this stuff?: http://www.blackfiveservices.co.uk/separate.shtml
but if it is too tricky, i would definitively go for python & PIL (pillow), here is a point to start: https://stackoverflow.com/questions/14088375/how-can-i-convert-rgb-to-cmyk-and-vice-versa-in-python