First of all , Itachi wasnt talking to Danzo or the elders , his very appearance was the message for them like "Im still here , be careful what you are doing".
About kisame knowing Itachi's alliance with the leaf , i am not sure about it.
There are 3 options:
1.Itachi fooled kisame and he didnt know anything about it
2.Kisame knew about alliance but he didnt told madara about it
3.Kisame knew about the alliance and he told madara , but madara didnt do anything since he was kinda scared , wich we can see after itachis death when he told that they no longer need to stay out of konoha like they needed when itachi was alive.
My personal opinion is that Itachi fooled Kisame and that he didnt know anything about it and that's why he was pretending to be after Naruto when infiltrating Konoha .
And no , Itachi didnt have Kisame in his genjutsu for sure