How debunked? The operators say they were told to stand down. Nobody denies they were told to stand down; the only denials are that this order originated from Obama or State (which isn't even in the CIA's chain of command.) The issue is who ultimately gave the order, and in that the guest is no doubt correct. Sending only three shooters can easily be counterproductive.
It may not even have been with any real hope of getting the locals to help. It's at least as important to find out where they are, so that even if they aren't helping, the two sides (CIA operators and Libyan "security") aren't shooting at each other. That's an important thing because it's theoretically possible that the assault poses no danger but casualties result from the reaction force engaging/being engaged by the security force. In fact, that was a popular Viet Cong tactic - slip between two enemy units, make a lot of noise without taking much personal risk, then slip out while they fire at each other and hopefully call in arty or air strikes on each other.
But either way, the operators' claims are not in conflict with Lane's interpretation, unless one assumes that all stand down orders are issued from the President. (Or I suppose, one assumes that a stand down order necessarily means we're sitting this one out rather than don't do anything right now.) This is merely Media Matters running cover for Obama when he doesn't even need it.