I did exactly this, put it in a 2U case. Fantastic performance, but even with the best Noctua I could put on it the CPU fan sounds like a Hawker Harrier doing VTOL when it's under load. Don't regret the board, but wish my rack was in another room now.
You can adjust some fan settings in the BIOS, like what temperature it starts turning on, the PWM setting when it first turns on, and the temperature at which it hits PWM of 100%. After tuning those a bit, mine is pretty quiet unless I'm compiling with all cores or something.