I definitely can sympathise with Kudou. He's hating himself for slowly falling in love with someone who looks like Kujirai but isn't and also, because he thinks he's betraying her. And the fact that Kujirai is there, having the same face as her annoys him, and makes him question if she had any part to the disappearance of Kujirai-A.
This coming after the chapter where he sees the difference in Kujirai's bedroom and personality hits even harder as this feeling of dread has slowly built up and the fact that he's seeing a lie right in front of him is unsettling. It's not Kujirai's fault but man, I can see why he would say something like that.
He obviously doesn't HATE her in a sense.