This is in response mainly to your edit.
At 100% CPU utilization 2.1 GHz is completely expected I really don't know where you're getting that 3.9GHz is the base speed of your processor as that's not listed on the spec sheet at all. The 4.1GHz is the Max Turbo Frequency and you'll only ever get that if you're using under 50% of your processor power.
There is no way that a 6 core 12 thread laptop processor is going to be hitting even close to is max because of heat those extra 2 cores are going to turn that thing into a furnace at even 3.5GHz.
I know you said in another comment that you don't believe its a heat issue but you have to be wrong about that because that would be the only reason the processor is clocking down to its true base is to maintain heat. Download Real Temp Extract it to a random folder and run "RealTempGT.exe" the GT version is very important to select as that is the one that will measure all 6 cores of your processor.
Check what your GHz are and what your temps are before you launch Destiny and then check again what they are after you launch it. I am pretty confident you'll see a heat spike into the 70s and slowly climb into the 80s and at the same rate you'll start to see your GHz clock down and down till it gets to just 2.1GHz.