I just noticed a little caveat on my suggestion of copying over Main.sublime-menu and editing it. It'll use the updated settings when you select the Clojure REPL from the menu (Tools > SublimeREPL > Clojure > Clojure), but if you start the REPL from the command palette (cmd-shift-P) then it'll use the original settings file from the package and ignore your edited version.
If you want to be able to use your new settings with keyboard shortcuts or the command palette, I only know of two options:
* edit the SublimeREPL package files in-place (I try to avoid this).
* copy over the whole config/Clojure directory from the SublimeREPL package to the User package, and edit the files so that you have a new lein2 command which is named differently from the existing Clojure commands.
I can't figure out how to customize the existing Clojure REPL commands solely from the User package; copying all the files and leaving them as-is ends up just making duplicates of the commands.