While the world seems extremely sensitive to such things recently, I would not expect this to be an issue in most of South America. It is a vast continent and there are tons of different communities, many who live quite isolated with their own specific dress. Even in the more cosmopolitan cities, people wear all sorts of clothes with subtle difference that locals understand and they often make presumptions based on what is worn.
The keffiyeh is rarely seen in South America and would certainly not be recognized so readily as it would in the middle east and Africa. For sure, it will be noticed but I suspect it won't be interpreted as a political statement as related issues are not as well known, unless you stumble into a particular community of middle-eastern decent.
It is impossible to say that no one will be offended but it is unlikely. I have lived in South America and have been to most countries on that continent.