The doc functionality calls clojure.repl/doc. For clojure 1.2.x it is (I beleive) clojure.core/doc.
It would be almost trivial to fix this, but nrepl.el should consider the Clojure version and behave appropriately. Given that there is Clojure code embedded in the elisp source.
It is essential mainly for the future when our current code will be outdated - no one knows who will support what, and for how long, and when it would die. (compojure is 1.2.x nowadays). And generally, I don't feel comfortable seeing embedded strings waiting to be evaluated in a foreign interpreter.
What are your thoughts on externalizing the Clojure code out of the elisp code?
Sorry about the long overdue response. I dislike a lot the embedding of Clojure code in Emacs Lisp code and I think the best way to get a handle on this would be to employ a standard middleware that'd be required for nrepl.el to operate. This would make supporting multiple Clojure versions extremely easier and would simplify quite a lot the Elisp codebase as well. Hopefully I'll start working on this middleware before the year's end.