emacs has debugging, IntelliJ+Cursive has debugging, Eclipse, and others. A google search for any of these will yield more information. I use intelliJ and its debugger is full featured and nice, allowing you to put breakpoints even in clojure and java core code.
Initially I used a debugger with clojure, and every few months I pull it out when the problem seems to warrant it. But debuggers are not all they are cracked up to be. For example, when dealing with async code, a debugger is not very helpful. REPL-driven (and test-driven) development is a big advantage over the traditional "compile and run" process that a language like java requires, and almost eliminates the need for a debugger.
Clojure stack traces are just java stack traces, with clojure code mixed in. If a java stack trace doesn't make your eyes bleed, a clojure one shouldn't be much worse. The problem with stack traces seems to be that people don't actually read them.
I would disagree with your comments about Java; Java has many positives, first and foremost its ubiquity resulting from "write once, run anywhere," some very good core libraries, and more. But refactoring and debugging are (almost) completely unrelated to the language itself. And I'd say Clojure's tooling is pretty simple. Dependencies are handled easily. In short, you don't choose a language because of a debugger, though the editors/IDEs mentioned above have some good ones available.
We run clojure on huge, major production systems that span the world, and many other companies do too. The java ecosystem provides a particularly well suited host for clojure for critical systems.
Imagine a newcomer debugging a bug from clojure someone else has written...
A newcomer learning clojure and debugging some code may in certain situations want to use one of the debuggers mentioned above, but in most cases he or she will be better served by understanding what's going on first, developing a closer familiarity with clojure, and only then resorting to a debugger.