I do not know whether there is legal precedent for a person's refusal to submit to a polygraph interrogation being used as grounds for denying permanent residency/citizenship. I haven't heard of it happening. A person's refusal to submit to a polygraph examination is not admissible as evidence in the federal criminal courts, but I don't know if the same holds true in immigration court.

As for "black marks" on your report, it seems to me that being the subject of an espionage investigation is already a "black mark."

I suggest that you discuss your U.S. residency status, and the FBI's threat, with your lawyer.