ClojureScript doesn't have all of Clojure's reference types (just atom, I think) nor STM (yet?) so yes, you do lose something. I would also guess that while (fib 36) might be faster, you would see different results for more realistic programs. Gambit Scheme's garbage collector might not be as strong as HotSpot, which I gather is quite good for long running apps. ClojureScript also doesn't have runtime eval, so you lose that too.
For command-line programs, this could be pretty rad, as is ClojureScript on V8. It's also just cool :)