I know some of the older H100s had issues with this.
The PSUs put out 12v plus/minus 5% - which is within ATX specification.
So, your PSU could be putting out 12.6v on the twelve volt rail. Now this doesn't necessarily damage any components so it isn't a fault, but it would make the pump spin up to 5% faster which can cause it to rattle/spin unevenly.
I haven't heard this happen with the new hydro series though, so I would double check to make sure that this is definitely the problem.
I had an H80 that did this, and I attached the 9v resistor that comes with the SP120 QE fans and it completely stopped any noise at all, and the temperatures weren't really affected at all - although it probably isn't recommended you do this.
If you got a molex extension, and then a molex to SATA converter, you could cut the 12v wire of the molex extension, and solder in a 12v resistor. This would limit the voltage to 12v even if the PSU was outputting 12.6v which would hopefully solve the problem. That's probably the best way to go about it, and soldering a little wire such as that wouldn't be difficult at all.
The issue with using a fan controller is that a lot of them work by constantly applying the maximum voltage, but rapidly turning the power on and off, rather than directly reducing the voltages. You don't really want the pump to be rapidly turned on and off in this manner as it could damage it, and if it's still receiving 12.6v to it, I'd guess there's still a small chance of the problem reoccurring.