Yes, you can use a fan controller.
As you have just learned, the manufacturer's stated noise level is overly optimistic. It does not match reality. Happens all the time. Most of the noise is caused by air moving through, over, under, and around parts.
You do have another possible solution. If you purchase a fan controller and reduce the rpm to reduce the noise, then you will also be reducing airflow and cooling capacity. Why not simply just buy a better fan in say the 800 or even the 1200 rpm range and install it?