I agree with Flavius that the Autarch can be armed with three weapons.
Though I have heard the argument that the pistol is "obviously" upgraded, who's to even say that it would be the pistol that would get replaced? If I bought my Autarch a Reaper Launcher and nothing else, could anyone argue based on the rules that if I wanted to move and fire, I no longer have my pistol, much like the Eldar Rangers/Pathfinders carry both a Long Rifle and a Pistol?
An argument against the Autarch carrying all three weapons would thus be suggesting that the pistol disappears if and only if two other weapons are bought, and such a conclusion is not supported by the rules.
It may be that this was an error on the codex writers' part... but it could have very well been intentional. Why include the pistol as standard wargear, when it's a 1-point wargear option for almost every other IC out there?
Sure, there is little if any precedent in 40k for a character being able to switch his two-handed gun out for two different one-handed weapons in assault. But hey, if anyone could do it, I would certainly vote for the Eldar master of battle...
(Sorry for ranting on this as if someone was taking a hard line on the other side in this thread... but I've already had this debate live...
)