I think the issue will be compiling it for the CLR and then distributing it. The current script gets and runs a JAR, but I 'd imagine it would be relatively trivial to modify the script to run the CLR instead - but you'd have to build from the source included in the JAR (if it's all there...)
Haven't had much experience with it myself, it has been a while since I've played with Clojure.
Maybe once Light Table is somewhat stable, someone can hack it to use ClojureCLR for the benefit of the security-conscious Windows users :)
I really should get involved in open source projects.