If your program is able to utilize all the cores and its threads then two quadcores and 16 threads is definitely better than one quad with 8 threads. You can overclock the Xeon to match the i7-950 clock speed which will then make it twice as fast or able to do twice as much calculation. Thats if you can keep the CPUs cool enough and have enough RAM.
Very few, if any, server motherboard allows for overclocking. Besides you want a very stable system, not one that may crash after a couple days of running and then you have to start all over again. I would also recommend ECC memory which requires the use of Xeon processors.