It looks like we'll need to add a processContent-like callback to the cssjanus grunt module to alter the include, or maybe a option to cssjanus to RTL'ise all include filenames it runs into.
I'm attaching my attempt at doing this, but it's not working. I'm not sure why, but color-schemes/*/colors-rtl.min.css appears to contain too much data, but colors-rtl.css and colors.min.css are fine.
Obviously, the -rtl.min includes the .min instead of the RTL version still since I couldn't figure out a way to process the content without altering something other than the grunt file.
I don't actually know what I'm doing with Grunt here.. so feel free to ignore the patch :)