Obito using him is quite different from manipulating him. I agree that both Obito and Orochimaru used Sasuke, but Sasuke got more out of both of those. He used Obito not only to extract his revenge, but also to gain EMS, while all Obito got out of it was one of the Hachibi's tentacles. Sasuke fought for his own side. It was merely that they all had similar goals, so both sides benefited. But it was made clear with both Orochimaru and Obito that Sasuke was only playing along until he got what he wanted. His intentions to betray them was there from the start.
As for Kabuto, the only time I can recall that he was open to attack was during the White Rage technique, and I don't know how that would qualify. And Kabuto was attempting to take back control of Itachi, quite early on in that battle.
Naruto's "warning" was completely stupid and there was no reason to listen to it. Naruto didn't explain anything. If anything, had the Juubi been taken care of fast enough, the war would have been over and a lot of people wouldn't be dead. I would point out that Sasuke wasn't the only one fighting to kill the Juubi. So were the Hokages, so clearly it wasn't a bad decision.