By questioning Mayella about her life at home, allowing Bob Ewell to show his temper on the stand, and allowing Tom to both tell his story and to demonstrate how injured his hand is, Atticus is trying to first of all prove that Tom is the least likely suspect to have beaten up Mayella. Beyond this, Atticus is trying to show that it was Bob Ewell who beat up his own daughter. Atticus is demonstrating that Mayella was a lonely girl with few goals and no prospects. Her family was uncomforting, and her life boring. Chatting to Tom gave her some feeling of connection to the outside world. Flirting with Tom gave her a sense of power and feminitity. Kissing Tom would increase all of these things. However, Bob Ewell - even more prejudice than most of the town - wasn't going to stand for that. He understood that Tom wasn't trying to rape his daughter, but Bob didn't want anyone to think that a member of his family was consorting with a black man. He beat Mayella for disgracing him, and he trumped up the charges against Tom to make sure his family "honor" was intact. The liars in the courtroom are Mayella and Bob.
If i can understand your question correctly, Atticus is trying to tell the jury that Mayella wasnt raped. Especially if she willingly kissed Tom.