Ah, I think I understand your problem now, thanks for clarifying. I think what you want to do is delay the compilation of the Clojure code that depends on compiled Java.
You could do this by moving your Clojure code that depends on Java into a namespace other than your build.boot. Then in your build.boot, require that namespace only after the Java has compiled. Does that make sense?
I'll have time later to add example code to this post.