Check that you have the latest BIOS for the laptop, this is an area where manufacturers make improvements over time as there is more user experience with the machine. Worth checking anyway for any other improvements that you might benefit from.
Doesn't this machine have a 'whisper mode' when the fan switches to a low speed and the processor runs slower to reduce heat build up? If this profile suits the laptop and your requirements it may provide some mitigation if the problem is just that the replacement fan is a bit noisier than the original (fans the same size can have quite different performance characteristics in throughput, noise and speed as well as different construction and bearings so a like-for-like replacement is quite difficult, leaving aside that even two fans of the same model from the same maker may not behave in just the same way).
Indeed it does have the whisper mode button. And while it's not the solution I was looking for (and I did know about the button when posting the question), it seems it's the only reliable way to cut down the noise a little bit.
The fan still spins up when CPU usage is high but the noise levels are generally lower in this mode. Performance, of course, is also lower. – Tomas Andrle – 2009-07-27T21:59:50.183