The clock frequency is no measure of computer power, it's just to please the masses, so in the current rates computers could still be crap by the time the Shivans invaded our systems.
And indeed the physical limits for standard transistor-based processor manufacturing are real close. Next generation computers (and by next-generation I really mean next generation, and not the next frequency level) will probably use Single Electron Transistors, while the next generations to come will probably evolve to multi-level logic, non-deterministic analogic processing, and quantum computing, in this order. And you don't get any faster than a quantum computer (as soon as you have the problem modelled on it, the answer will be instantaneous).
So, there you have an idea. The terrans could quite possibly be using quantum computers, but may have not been able to model a truly AI program, and hence the pilots are still needed. Or they may have stuck on the standard transistors and have the same computing power as today's processors, who knows...