It would seem so, and I apologize. I think that this bit:
> The democracy the FBI is sworn to protect has turned on it. What is left for it to protect? The laws handed down from an older, wiser time? Perhaps the time of Senator McCarthy? Or Jim Crow?
specifically mentions of McCarthy and Jim Crow, made me misunderstand this bit:
> What if today's president pardons common criminals and today's Congress legalizes their crimes—will the FBI continue to enforce yesterday's laws?
That is, the first part made me think of Bad Laws created by Bad People, and this made me parse the final question as: "What if today's president and Congress turn into Bad People and make Bad Laws, should the FBI enforce such Bad Laws, even when they're obviously just like Bad Laws from Bad People of the dark chapter of our past?".
The point I'm making is, yes, the FBI has to enforce law, good or bad, because that's the reason it exists. If it starts getting picky, it invalidates its own mandate.
Also, FBI as an organization is not an independent entity that sworn fealty to the government - it is a construct of the government. Therefore, if "The democracy the FBI is sworn to protect has turned on it", what the FBI should do, as an organization, is to lie down and take the beating, and allow itself to be disbanded. The FBI was created to protect democracy (in specific ways), has sworn to do it, so if the democracy decides it no longer needs the FBI, then the sworn duty of the FBI is to stop existing. For the FBI to do otherwise is to break the oath and invalidate its own existence.
(Now this applies to the organization. As for the people in it, they're also citizens with conscience, and they're free to work within the process to right what they see as morally wrong, and/or quit.)