You've accurately identified the timeout. CIDER (nrepl, in fact) first tries to interrupt the thread in a "legal" way, but if that doesn't succeed, it waits for 5 seconds and then kills the thread forcefully. It is not very "safe", might potentially corrupt memory or screw up locks, that's why it's a last resort, but it is totally fine to do that during development.
Welcome to Clojure! Hope you have fun.