Hmm, interesting. I would still give it to Itachi. Im a huge Itachi fan but I'm not a fanboy (I think rationally).
While I'm not disputing Kisame's power (hes one of the stronger Akatsuki), I would say Itachi will most likely outwit him. As Samehada isnt affected by genjutsu, Itachi's Plan A goes out the window. But, looking at Itachi's record of finding a weakness against jutsus (his greatest feat was when he found a way to defeat Chibuka Tensei), I would say he'll find a way out of the water prison.
Anyway, we havent even witnessed Itachi's taijutsu. In the official databook, Itachi's taijutsu is 4.5, while Rock Lee's is 4 in volumes 14 to 27 (Second databook). Rock Lee has opened 6 gates and we've seen his drunken fist style by volume 27, and Rock Lee still gets a 4, while Itachi gets 4.5. I wouldnt be quick to dismiss Itachi's taijutsu.
Even if you take the taijutsu out, although it IS a major factor, I would still say Itachi wins due to superior intellect. He'll find a way, he always does. On top of all this, Kisame himself admitted he couldnt beat Itachi (cant be bothered to find the page). I would say Itachi with max/near death difficulty.
All this being said, I truly respect Kisame and think he is a kickass character who, I think, deserved more chapter/screen time. He's a hugely formidable opponent on his own. Add Samehada into the mix and you get a monster fighter whos unaffected by genjutsu and ninjutsu. Im sure you will think this is a fanboy's response, but Itachi's intelligence is unquestionable. He figured out a way to beat Chibuka Tensei ffs!!! A technique used by the Sage of Six Paths himself (although on a bigger scale)!!! Itachi will find a way.