I think it only strikes people as racist who are either racist themselves, or are hypersensitive to and looking for racism.
The essense of predjudice or bias against people of another skin color, ethnic group, etc. is to judge them based on that factor. To be truly unbiased, however one has to not flip it on it's head, and say that because Rudy has dark skin, for example, that means that he isn't more likely to commit the crime due to other factors. These people are so rampantly looking for bias in their attempts to support their own bias against Knox and Sollecito, they put the tag on them as "blaming the black guy", despite having zero objective evidence of that. For example, is Knox saying she had visions that Lumumba committed the crime, when it turned out to be Guede, evidence that Knox is racist, or is it evidence that her accusers are? When she made those statements, she didn't know Guede was the killer. It is a coincidence that both have dark skin, yet Amanda's accusers immediately assume she did that on purspose. I see that as being racist against not only blacks (they are equating the two men because of skin color), but also against Amanda (assuming a white girl would have racist thoughts, even though there is no history of that with her).
Getting back to the specific example, Hellmann is saying that Rudy had no connection to Amanda and Raffaele. This would have been true if Rudy was white, or any other race. He is saying there is no evidence they were friends, and no evidence of phone calls or other types of things they would have had to do to communicate and plan the meeting at the cottage. Rudy is an unemployed "drifter" (for lack of a better word), and AK and RS are college students from out of town. Rudy goes around breaking into buildings, they have jobs or wealthy parents and go to school. Nowhere in any of that analysis do we even need to know what skin color any of them are, and the case can be made (as Hellmann did) that it is unlikely that the three would commit a murder together, especially on the spur of the moment.
The only place I can find racism there is for those who know the skin color of each person involved, and let their own prejudices make assumptions about each person's behavior. You don't have to have any racial prejudice to tell that the prosecution theory is bogus from the get go.