Yeah, you'd need to replace all the fans, and you would still need to have the RPM generator as mentioned above to make sure the switch actually boots (as it won't boot if the RPM is too low)I assume I would need one of the Noctuas for each fan so a total of 3 in my case? In my 6610 I have 3 fans. 1 for the PSU and I assume two generic fans.
Personally I'd be more inclined to use this with the existing fans.
Just split the PWM signal to each of the fans and use the temperature sensor as a "fail-safe" in case of fan-failure. This way the other fans would receive a higher duty cycle and increase fan speed accordingly.
You could of course also get more silent fans (but this would be a lot more expensive compared to 5-6 USD), and use the same approach unless you want run them on full blast at all times.