I agree. Padmé being explicitly told that he slaughtered a village and being understanding, of all things, is the most unbelievable thing about their relationship to me. I feel Anakin should have glossed over it, or pretended he didn’t remember. That way, all Padmé knows is that he felt immense anger, but doesn’t know if he acted on it - so she could still say the line and have it fit naturally. However, thematically it would probably have been better if there had been a way for Palpatine to say that to him somehow.
He says things along the same line in ROTS anyway (“It is only natural… he cut off your arm, you wanted revenge”).