I don't think you're going to be able to easily do this. JPEG isn't like GIF where there's a single palate of colors that you can just change in one place. You'd basically have to convert the JPEG into another format, change the color in the uncompressed image, and then re-compress back to JPEG. And due to the lossy nature of JPEG compression your going to get a worse (how bad depends on the quality setting used) converted picture.

But yeah, Image::Magick and or GD's the stuff to look into. Or possibly script the Gimp.