In my view (and in agreement with Buffy's answer), it is inappropriate and rather unfair to penalise someone for their "accent" (presumably you mean their "pronunciation"; having an accent which does not impede correct pronunciation, is generally not a problem). This is true even if what they say sounds like complete gibberish to anyone in the audience.
However, it is also entirely fair to point out that this is a non-trivial issue, and that the presenter shouldn't just shrug it off simply as "this is how I speak".
There is a lot of nonchalance when it comes to putting an effort to correcting one's accent, when it is actually a big obstacle to effective communication, and pointing out that, it is in fact a problem that could be worked on going forward, is more than fair.
With regard to such a presentational context specifically, while it may be unfair to comment on what their accent is like 'now' -- since they have little control over it in the short-term -- it is not unfair to point out that they should work on it, and that, in the meantime, it is a limitation they should be aware of, and try to mitigate against in their presentation. Therefore, what you could mark, is the extent to which the rest of the presentation showed an effort to overcome this limitation, by using appropriate visuals, quotes of the important phrases, logical flow of slides and argumentation, etc. If, given their 'limitation', they failed to convey their message "because" of their presentation, rather than "despite" of it, then it is fair (or at least "less unfair" * ) to reflect this in the marking.
This should hopefully encourage the student to both improve on their presentation technique, as well as point out that language is an issue that deserves to be improved in its own right (if possible).
*: there is still a degree of "unfairness" if you do that, in that other students would not have had to make the same effort, so I would treat carefully even with that. If you penalise someone on that basis, it should be minimal, and according to a marking scheme that would have affected other students equally.
"Is this racist?"
Having said that, just to address the "is this racist" point. Consider this thought experiment.
You are a student, who's been chosen to represent your university in an international competition, taking place in, say, China. The competition itself is in English, but, as it happens, it turns out that this year most of your competing presenters who made it to the finals, are from Asian-speaking countries. When it's your turn to present, you naturally speak in flawless Queen's English, but as a result, the large majority of your audience and panel who is more used to "Chinese English" fails to understand you. Meanwhile, they were perfectly comfortable understanding the other presenters.
You finish last, and the feedback on your card was "sorry, we just couldn't understand you; perhaps you could work on trying to sound more 'Chinese' when you speak".
But, would you also accept that, given the context, your inability to speak in a way that would make you understood, while 'not your fault', is still in fact 'a problem'?
What if the organisers had warned you of this before the competition? Wouldn't you have made sure your slides and flow of presentation could make up for that fact so as to minimize the impact? And if you hadn't made that effort, would your disqualification still feel as unfair?