By posing this very question, you are reading the novel "against the grain" or are reading as what is called a "resisting reader," which can be a very good and challenging way to read. I'm not sure that it is possible to marshall solid evidence that Tom Robinson indeed raped Mayella, but it is possible, as your question asks us to do, to resist the novel's promptings and to challenge the standard reading of the novel that Mayella is wholly guilty and Tom is wholly innocent.
(I would recommend that someone begin to read the novel "against the grain" only after they are certain that they have fully understood the standard reading and want to take things one step further. This strategy is a way to attempt to raise and answer questions that are not normally asked, but it's not the place to start when we first pick up a novel.)
We might begin by arguing that the novel is not an objective account of anything; if it were an objective account, how would we make sense of the opening, strongly nostalgic statements about how "it was hotter then" and "people moved slowly then"? Rather than offering an objective account, the novel instills in the reader certain biases and steers the reader toward certain conclusions. We are supposed to like (and to believe) the Finches, for example, and we are not supposed to like (or to believe) the Ewells. In reviewing the novel with this bias in mind, you are certain to find mutliple instances (the "evidence") of how the reader is not given a neutral account of the whole event.
Of course, we might then have to acknowledge that in the American court of law, the burden of proof is on the accuser and -- at least in the account that we are given -- that the accuser did not deliver that proof in court.
In the end, then, we might not be able to convince anyone that Tom Robinson indeed raped Mayella, but we might be able to cast some doubt on the standard reading of the novel. Like the jury, which quickly handed out a guilty verdict although there was inadequate evidence, the standard reading of To Kill a Mockingbird may arrive prematurely at a conclusion -- a certainty in Tom Robinson's innocence (which is much more than the legal pronouncement of "not guilty") -- that itself remains open to questions.