Captain Katanga was a black guy, and he was one of the smartest people in Raiders. And there's nothing wrong with the depiction of the Arabs. I think you're way over-thinking the subject.
Excessive concern about the depiction of race and gender in movies will only lead to every villain being played by a white Englishman.
You're right that Katanga is one of the most fleshed out non-white characters - he has what, four lines? The issue I have with the depiction of 'the Arabs', is that it's just that - virtually none of them are characters, and the ones that are are stereotypically comic.
The issue is not their villainy, it's the lack of attention to them as characters. I presume your comment about white Englishmen is sarcastic (it's sometimes hard to tell on the internet), because that's precisely the kind of lazy stereotyping that I'm calling out. We telegraph everything you need to know about a character into the common beliefs we have about the characteristics of their race and gender. We even see this with the monkey spy - how does the movie signal that he is untrustworthy? He's dressed like an Arab...