I tried replacing the 500GB Seagate drive in my late 2009 21.5" iMac, with a 1.5TB drive, also from Seagate. But I had the same problem with the fan slowly reaching full speed. So I had to swap back the 500GB drive for the time being.
At least with Seagate drives, the connector for the thermal sensor cable is normally used as a jumper block for speed selection. See page 20 of this: http://www.seagate.com/staticfiles/support/disc/manuals/desktop/Barracuda%207200.11/100452348b.pdf
Apple-branded Seagate drives have custom firmware to change the function of the jumper block.
To install a non-Apple branded drive, you need an external sensor cable, the same type used in iMac prior to October 2009. I have ordered P/N 922-9214 for my mac and will install it together with my new drive once I receive it.