You can write a script to check the CPU temps in linux and set the fans to kick on at different power levels for certain temps and just run it as a timer event. I did this for a Macbook I had Arch running on when it was running hotter than I liked.

Could you share your setup? There are so many tools available for tuning of power use and fans. It's hard to pick the right one.

I'd prefer to run my laptop with as few fan activity as possible without overheating. So when the CPU gets too hot, clock it down instead of starting the fan.

I completely agree with that when I'm using the laptop unplugged, especially if it's on my lap and I want to get maximum battery life.

However, if I'm sitting at a desk where it's plugged in I would like to get as much performance out of it as I can.

Actually there is - look at the last paragraph of the article. You can configure the max temperature for when you're connected to power and working on the battery.