Your system is just fine. Turbo Boost is an feature that allows the CPU to dynamically raise its clock speed depending on the current system activity (less cores active = higher clock). The CPU monitors its own power consumption and heat output and will only turbo when it's safe. You're perfectly fine leaving that feature on. It's intended to work perfectly fine with Intel's stock HSF.
Turbo boost is "stock". It is what the chip is designed to do. A 2500K not overclocked runs at 3.4Ghz with 4 cores, 3.5Ghz with 3 cores, 3.6Ghz with 2 cores and 3.7Ghz with a single core active. Basically, you should never see your CPU at 3.3GHz because it should always either be idle at 1.6GHz or Turbo'd to 3.4-3.7GHz.
Most people turn Turbo off when overclocking. Some people overclock through Turbo. Neither way is incorrect. Personally I have Turbo off but I left power savings on. So my chip is either in low power mode or all 4 cores/ 8 threads are maxed.