If we discover a violation of zero tolerance item (a Freddie Mac fee) on a good faith estimate (GFE), and more than thirty days have passed, what should we do to correct the violation?

Because it has been more than thirty days since the zero-tolerance violation you identified, refunding won’t cure the violation. That said, you are bound by the GFE, and it would probably be best practice to refund to mitigate any arguable penalties for the violation. 12 CFR  1024.7(f).