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Presumably Kayaba knew/felt he should be punished for the actions--after all, he set himself up to be the final boss, and if the "echo" of him in the ALO arc is any indication, set himself up under the same death game rules for that final boss fight like everyone else, so that the person who killed his avatar would kill him as well.
Also, I don't know if anyone's brought this up yet, but I do think part of the reason why Kirito wasn't openly hostile to Kayaba in ALO is both because he had just aided Kirito in defeating Sugou to save Asuna, and because he had inadvertently gotten to know Kayaba as a person due to their interactions as Heathcliff--how do we know that Kayaba changed his personality to be Heathcliff? The echo was pretty reasonable as a person (so to speak), and so was Heathcliff--after all, after getting Kirito to join his guild only for someone to murder a comrade before making an attempt on him, Kirito says he and Asuna are going on vacation and he's like "That's fine, you deserve it after that crap. Sorry."
So I do believe that Kirito knows that Kayaba is a monster, but he for a good deal of time got to see Kayaba as a person. And that person went and aided Kirito when for all intents and purposes he didn't have to.
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