It really isn't, and I'm not sure why he chose to criticize the CIA during a presidential run. It is in the same vein as a lot of other things he goes after (that is, done on a basis of principles instead of what-issues-can-I-win-elections-on), but I feel like there wasn't much need to sound off on the CIA's policies. It's not just grandstanding -- scaling back the CIA's level of interventionism is no doubt going to happen under his hypothetical presidency, because it doesn't fit in the slightest with his noninterventionist foreign policy -- but it also doesn't make much sense. Just run on the strict noninterventionist policy platform like always instead of calling attention to something that'll get you labeled a conspiracy theorist, I say.
I do maintain he's not being a conspiracy theorist here, though. Tolstoy already explained how what he actually said was indeed happening. And if you accept that the "CIA coup" was a (badly executed) rhetorical device instead of a literal conspiracy claim, I don't think what he said was really that controversial.
The misrepresentation comes not from what he actually said (see last paragraph) but from stories accompanying them that say things like this:
"I think the military would laugh at the notion that they take orders from the CIA. They take orders from the President and are accountable to Congress. We know this, because we’re rational adults and not conspiracy theorists."
Where the author takes that rhetorical device literally, labels him a conspiracy theorist, and on top of that gets things factually wrong -- for one, the Afghan War was basically run by the CIA, as Tolstoy noted already.
It doesn't help that the author is clearly and unequivocally biased. There was no attempt whatsoever to interpret what Paul was saying in anything more than the most extreme light. Unfortunately, that's a far more universal criticism of reporting today than I'd like to think.