Plus, if Charlie is discovered lying, it would destroy his chances at a law degree (I think Oliver Platt told him if he did nothing wrong, said nothing wrong, and saw nothing wrong, his defense would cost $100,000…he urged him to make a deal.) Jed wasn’t going to bring anyone else down with him…that’s why he accepted sanction.
And can I just say, the Latin-laced God cursing in Two Cathedrals gives me the chills to this day? Damn, Sorkin can write.
Exactly. There wasn’t any grand conspiracy UNTIL then, why the hell would he want to manufacture one now?
Quite so. But I still think he wanted to forestall Charlie’s possible lying to protect him, because of all the staff Charlie’s in the worst position.
I assumed that Jed was talking about questions like, “Have you ever seen the POTUS pass out?” or “Have you ever seen his hand shake?” or “Were you present when Event A and B happened.” Charlie, more than anybody else on staff, would be privy to those moments, and it would probably seem pretty easy to simply say, “No, I never saw him shake when he signed his name.” Small lies that might seem like they’re unprovable, one way or the other, but not worth the risk to Charlie’s future.
Enlighten us. 
My guess would be Jimmy Carter. A decent man who was in way over his head.