If they are saying that he was killed due solely or primarily to racial prejudice, that's a distortion. But most religious conflicts have, or develop, an ethnic component. The Romans almost certainly looked different from the Jews, and it wouldn't surprise me if the Pharisees were lighter-skinned, or otherwise had distinct features, from other groups of Jews. Most cultures with a caste system base it in part on appearance, because otherwise it would be too easy to "pass."
Not to mention that half of Jesus' genes came directly from God the Father, so there's no reason to believe he was the exact same hue as Mary. It's a detail as unimportant as whether he was short or tall. If Jesus didn't look like Jean-Claude LaMarre (pictured), he almost certainly didn't look like Jim Caviezel, either.
If the movie doesn't distort the central message of Christ's sacrifice, and helps bring it to a new audience, I don't see the problem. Just as I didn't have a problem with The Last Temptation of Christ or The Passion. Looking at the peripheral questions in new ways to find new insight or bring a new audience to the central message of the Gospels is as old as Christianity itself.