Simple, rely on the venerable rlwrap that provides you with a readline wrapper around your existing REPL.
My sucky REPL looked like this:
#!/bin/sh
java -cp PATH_TO/clojure.jar clojure.main $1
Simply install the rlwrap package using your favorite package manager and change your REPL script (clj) to the following:
#!/bin/sh
rlwrap java -cp PATH_TO/clojure.jar clojure.main $1
Major suckiness averted. The added boon of this approach is that you now get all the readline goodness (history traversal, inline editing, etc.) you've come to depend on in other REPLs.
