As Tom Robinson testifies, Mayella Ewell actually kissed him (and not the other way around), and she ordered him to kiss her back. He resisted and tried to run away, but she blocked the exit, and he did not want to push her out of the way or harm her in any way (as this would have been a death sentence for a black man).
Further, he could not really resist her advances effectively because he didn't "wanta be ugly" to her and incur her anger against him. Just then, her father got home and saw them through the window; he shouted at them and called his daughter a "whore," indicating his belief that she had slept with Tom. Just then, Tom took off running as fast as he could, and so he cannot report what happened after that.
Scout realizes that, as a black man, Tom really did not have a good option; his choice was simply untenable. If Tom pushed Mayella away, physically putting his hands on her in anything remotely resembling a forceful way, he would be signing his own death sentence; by staying there and returning her advances, it would result in a similar consequence; finally, he could just run away as soon as possible, but that would make him look guilty. He chose to run.