"Why is obtaining a "Yale" level of education in and of itself a good thing, especially if we're not seeing society-wide positive change driven solely by individuals with that level of education?"

If you don't think obtaining a Yale level of education is a good thing, simply don't go there? What would be the point in abolishing it?

"The article's point is that historically, large-scale change is driven by groups rather than individuals."

That would be the a) option, people can achieve the same things without Yale.

"99.999% of people don't have the choice to go to Yale. That would be true even if everyone in America were given "equal opportunity" from birth -- it's how scarcity works. The article answers this question for you in case you want to give it a second read."

Most people just decide not to go there. That doesn't imply that they don't have the choice.

"The article answers this question for you in case you want to give it a second read."

If their argument is it should be abolished because not everybody has the choice to go there, it is a bad argument. If b) holds, you would still want people to go to Yale to achieve the things that could not be achieved otherwise. And in case of a), it seems irrelevant.