I think there's a mixture of good, but misguided intentions, and the typical racist leanings of the era, however conscious or not they might be. I mean, I understand that Heston was cast in the lead role of an American. It was only after he brought up Welles that he decided to change the character to a Mexican "for political reasons". But with Heston already on board, I doubt they would've been willing to dump him, considering that he was the big star, but also because at the time, few studios would've dared to have a leading Latino actor in a film like this. So as much as I'd be willing to give some of this stuff a pass, it doesn't make it any less wrong.
But then there's the issue of the story, and how...
But then there's the issue of the story, and how...
WARNING: spoilers below
...the fact that the arrested Mexican ends up confessing sorta concedes that despite his methods, Quinlan was "right", so it doesn't really push forward any progressive agenda at all.