regarding the jinchuriiki, none of them except Naruto is an ally of Konoha. The shinobi nations aren't exactly at peace with one another; what was it, three years ago, that the sand ended up attacking konoha? What he is doing at those times is completely in line with "defending konoha", which is an admirable thing from the point of view of konoha.
regarding kakashi, if itachi had wanted to he could have ripped kakashi, guy, and whats-her-face to pieces with susann'o. He didn't, and no one died. If he is evil, what was the point of coming to Konoha?
regarding naruto... I dunno. To avoid looking like a softie in front of ol' shark face (who IS a true believer, after all), he had to have SOME, akatsuki-sanctioned, reason for coming to konoha. And who knows? He knew it was Jiraya with Naruto... perhaps if he had actually successfully abducted Naruto, he could have signaled Jiraya somehow, and the same thing that did happen, would have happened.
Think of him like an undercover cop. When you're working undercover, you have to pretend like you're a sonofabitch, ALL THE TIME. Sometimes, in really shitty situations, circumstances force your hand; either you have to do something that actually IS shitty, or blow your cover and get yourself killed, and then be powerless to prevent or at least ameliorate the situation that was so shitty in the first place.