Seeing questions like this so commonly I realize history is just a subject that is taught a 1/4 of the time in school but we never stop to understand what we are doing and for that there is a ton of wasted effort.
We can't know if he was guilty of the accused crime. Who would we ask? The same townspeople who tortured him without trial? They did not even know if he was able to be proven guilty, they acted on passion without hard evidence, and they can't tell us what they don't know (can't support). And here's the big issue, even if they did provide us sources that told us he was "guilty" we would still need to be critical to the point of disbelief of anything they said because they are biased. You are not ever reading a "factual account" when studying history, you are reading a story told seventh hand in the 200th iteration, always. And stories are made with agendas by people with prejudices.
If American society could not decide the facts then in the present, why would you trust it now a century removed to provide them?
Humans are hugely flawed and you simply can't always look at narratives to find your answers. This story is striking and leaves us with many questions but 'did he do it' should not be one of them and I'll explain why. You should not believe anyone that gives you that answer, especially considering... you need to decide for yourself based on the fragments of distorted information that are available.
Even this article is written with a slant or intention, it is clearly even an article in the first place (opposed to all the article-less lynchings) to be presented as a story about how cruel humans can be to each other especially over physical differences and perhaps how justice and wrath are easily confused. Every piece of "history" is recorded and retold for a similar reason. There needs to be a story, a lesson, something there to learn from. We never just read 500 years of mundane events, we instead collect stories to retell and there are always reasons why.
Now you have clearly (like many others I am sure) noticed something is conspicuously absent in the article: any mention at all of whether the accused was guilty or not or whether there was even any doubt. Well I can tell you that if there was anything suggesting he was innocent it most certainly would have been included in such an article. I can also tell you that when you dig into these parables they are often not as clean cut and easily understood as some crafty writers may want you to think.
In my own narrative he clearly was the number one suspect and very likely committed the crime but his atrocity is not of particular note when compared with the injustice carried out in response. In my own narrative he killed the girl but it doesn't matter and if he was innocent the story is exactly the same. The story is about a miscarriage of justice. It's like if a director left something unsaid by not showing a key scene, like in The Green Mile actually* I believe it is never addressed if the accused in that film is actually "guilty" but the story wouldn't really change either way.
We don't have time to go through and study every death, every birth, every victory, and every defeat. We need to choose the stories important to us.
History is not a record of events, it is the stories we tell ourselves about ourselves. It is our story, our legend. You won't find answers to hard questions when you study it, you may gain an understanding of who you and we are, what direction we came from, and perhaps even our general trajectory. What stories we tell and why we tell them are just as important as the content of those stories, the content is consistently flawed and nonfactual anyway and even hypothetically perfect sources would be interpreted incorrectly by our imperfect brains.