Short answer is yes. Multi threaded applicaitons will take advangate of the 6 core and perform the work "faster", however a dual core with a higher clock speed can outperform the lower clock speed of a 6 core assuming the application can't use more than two threads.
For example... In a non multi-threaded application a Phenom X2 overclocked to 3.5+GHz will outperform a stock Phenom X6 1075t at 3.0GHz. Using a multi-threaded application will tilt the other way and the X6 will shine. A balance between clock speed and cores is typically found in the X4 (overclocked of course).
As rolli59 said, you need to list the 2 CPUs, An Intel 2 core COULD be faster and better PER PROCESS than the 6 core. But the 6 core will obviously has more threads running at once, just because it's a 6 core CPU.
Note: I'm guessing you're buying the AMD Phenom II x6 1055T? In my opinion, just add 30 dollars for the 1100T Black edition