+1 I think it will be easy if we have the RTL rules inside each css file
e.g.
headers/layout.css - contains RTL rules for the layout
headers/icons.css") - contains RTL rules for the icons
headers/skin.default.css - contains RTL rules for the skin.default
headers/skin.dark.css - contains RTL rules for the skin.dark
headers/skin.organic.css - contains RTL rules for the skin.organic