I don't think John ever outright accused Natalie of pushing Marty. Based on her being at the scene of the crime and Marty insisting that it was her, he was suspicious of her, but he didn't absolutely accuse her of having done it. He had to follow up on what was presented to him.

Natalie has been acting like a baby throughout this whole ordeal. Even if she is innocent since she stood accused, she should have been hauled in for questioning, but wasn't. Despite the seriousness of what she was accused of, John still ultimately handled her with kid gloves. Maybe she did deserve an apology, but she didn't need to be smug about it and John shouldn't have "explained himself" to her when he gave it.

For a second, it seemed like he wasn't going to but of course he did. To not cower to Natalie demands would have added a kink to the Jolie reunion, and OF COURSE we CAN'T have THAT.