Mrs Weston is humorously asking Emma not to inflict physical violence on her. She has earlier suggested to Emma that Mr Knightley might marry Jane Fairfax:
"I have made a match between Mr. Knightley and Jane Fairfax. See the consequence of keeping you company!—What do you say to it?”
“Mr. Knightley and Jane Fairfax!” exclaimed Emma. “Dear Mrs. Weston, how could you think of such a thing?—Mr. Knightley!—Mr. Knightley must not marry!"
Emma, chapter XXVI
Emma objects rather vehemently to the idea of Mr Knightley's marrying Jane Fairfax, all the more so because she is unaware of her own desire to marry him. Naturally, at the first opportunity, she interrogates Mr Knightley about his feelings for Jane. Mrs Weston is a present during this conversation. Mr Knightley denies that he wants to marry Jane, and after he leaves, Emma immediately turns to Mrs Weston, expecting that she will eat crow. Instead, Mrs Weston says, effectively, that Mr Knightley doth protest too much, and his denial shows he really is in love with Jane Fairfax. She knows that Emma doesn't like being contradicted, and she knows how opposed Emma is to the idea of this match. So she laughingly says, "do not beat me" for persisting in my belief even though it both contradicts and offends you.
The rest of this answer constitutes spoilers. You have been warned.
One of the great joys of Emma is seeing how everyone filters their interpretations of situations through their own wishes. Emma herself is of course the prime example. But Mrs Weston herself is so desirous of a match between Emma and her stepson Frank Churchill, that (a) even when Emma reacts so strongly, she does not realize that Emma is in love with Mr Knightley (though to be fair, at this point, neither does Emma); and (b) she does not realize that it is Frank, and not Mr Knightley, who is in love with Jane.
Not even Mr Knightley is free of this blindness; he knows perfectly well that Jane is superior in personality and accomplishment to Emma, and he admires Jane highly, yet the possibility of marrying her does not cross his mind, and he never asks himself why. ("Because you're in love with Emma, eejit.") He realizes his love for Emma only when he thinks she's in love with Frank Churchill, just as Emma realizes her love for him only when she thinks he's in love with Harriet Smith (of all people).