Bear in mind, he has just tracked the Bounty Hunter there, so is under the impression that Dooku is behind Amidala's attempted assassination.

Even though, in my edit, he's not.

Although, I agree. The hostility at the level it is currently does seem a bit unjustified. It's as if Obi doesn't even take in what Dooku has just told him. He should at least question whether he's being told the truth or not. I don't know how this can be fixed though. This was a flaw in the original cut as well as mine.

I will have a go at shifting around the "I don't believe you" to replace the more hostile "I will never join you, Dooku" but I don't know if this can be pulled off effectively. I'd need another cutaway to replace it where it is originally. We'll see.