It may be the optify utility could do it. I haven't used it myself, but if it just moves everything in root in a deb and creates links then you should be good with that.

3+MB is certainly not an acceptable addition to rootfs for one theme. That said, i'd like to see this go into extras because it's a cool theme. Feel free to message me Lacedaemon if you have questions/problems setting up the deb to be optified. I'm getting so i can do it in my sleep.