Per the big files, its not so much Clojure but output at the REPL. Especially as a noob accidentally grabbing way to much data for a buffer is really easy, Emacs hangs, REPL and process dies and has to be rebooted and you have to bring up everything again. This is non-trivial friction when learning and should really be handled gracefully by the editor.
As for everything else regarding Emacs and learning all these points stand and are valid but still don't address the problem of someone wanting to learn Clojure and instead having to learn Emacs + Clojure + Cider. For someone just starting on the path most won't have more than 3 files of CLJ and may not even interact with Lein or Deps. Refactoring IS important but not to them. I just don't think the trade off is worth it for someone just toying around with CLJ in their free time. It may not be the best metric but "time to hello world" and "time to blog" matter to people coming in because it shows that the promise that they are sold is something that they can reach and achieve.