I have never heard any Clojure proponent encourage anyone to implement functionality at the Java level. I don't program in Clojure or Java, but it's obvious to me the idea is that the JVM is just the "operating system" for Clojure.
So you would not write hybrid Java and Clojure programs? You would not reuse and extend Java classes? Strange. I thought Rich went to the JVM because the eco system is so rich ;-) and not just because it happens to have a code execution environment and a garbage collection implementation.
When you're writing Clojure code, you generally are supposed to prefer Clojure features and idioms. Functions like proxy and gen-and-save-class exist because sometimes you have to create classes to use other Java APIs.