I mean on the one hand I kind of had it in the back of my mind that Itachi was not what he seemed. Kishi's done that enough times (with Kabuto and Tobi) that I've learned not to trust the first impression of a new character too much... but Itachi's not the lest bit new, thus why it was way in the back of my mind.
But if you think about it there have been some hints... for one thing, the fact that Sasuke did not actually see Itachi commit the murder. He only saw the illusion that Itachi showed to him, and I kind of suspected that Kishi did it that way for a reason, as it would have been much more dramatic for Sasuke to have actually witnessed the murder firsthand. Itachi was concealing something - either the fact that he didn't commit the murders at all, or the fact that he had help in it - and for some reason wanted Sasuke to believe that he had done it all on his own.
And I don't think Madara's after Sasuke's eyes at all... he's already got the "Ultimate Sharingan", remember? And it could even end up going to other way; Sasuke could end up taking his eyes and obtaining the permanent Mangekyou himself.
In any case I'm not the least bit annoyed by this, and in fact I am now waiting impatiently for the next chapter.