In my opinion the kinds of 'institutionalized racism' you're talking about are caused as much by bigotry, as it is caused by the actual policy implementations that aspire to 'fix' bigotry. While I agree that the state of things is 'bad', you can't get rid of something like that with affirmative action. All that does is lower the bar; the standards for admission and achievement. In the pursuit of statistics that make us 'feel good' we actively generate sources of validation for racism like the ones indicated in that article.

The theory is that [insert minority group here] are underrepresented due to unfounded discriminatory opinions of gate-keepers, and that there do exist sufficiently qualified members to fill a larger share of whatever group you're looking at. But that situation would be addressed by making selection race-blind, not race-preferential.

What happens when a large portion of minorities in a profession capacity are obviously and demonstrably sub-par, because they would have never been admitted/credentialed/hired on their merit only? At what point is that still [unjustified] racism when a particular race is clearly under-performing? If you're actively looking at race and using it as part of your selection rubric, you only increase their overall representation in the field by flooding it with under-qualified people of that aesthetic.

All this does is make comments like: "[minority] doctors are sub-par" or "[minority] engineers are sub-par" or "[minority] [anythings] are sub-par"* less and less racist, and more and more factual statements. Now you've created a legitimate reasoning to provide cover for more bigoted motivations of discrimination. And in fact, in the absence of any bigotry, still creating a situation where prudence demands discrimination. You're just trying to force numbers to look nicer in the short-term, at the cost of prolonging or even exacerbating discrimination into future generations.

If I'm an engineering HR manager, and I've found the last 3 [minority students] I've hired from [Affirmative-Action University] have produced sub-quality work compared with their similarly credential peers, I'm going to suspect that they have been given a positive handicap in some way, that their credentials are worth less because they're [minority], and that I can't trust that University to provide me accurate information on their qualifications. And so I will generally pass over [particular minority] graduates from that University.

Now, am I the racist one here, or is it the University's fault for distorting their own credentialing process to the point that I cannot trust it?

As an aside - I generally believe the lack of qualified people for merit-driven proportional representation is a result of poor K-12 schooling and upbringing (ie things like poverty), not anything significantly inherent to any race's genetics. But you don't fix that by letting them repeatedly fail to achieve their potential, and then lower the bar at 18 to let them in anyway. You have to go back and fix the problems at the source. And those barriers to achievement, more than anything else, seem to be a lack of two parents and general poverty. Which brings us full-circle to where I started. Address poverty, address poor schooling. Ignore race - racism will go away on its own if we do. Maybe not as quickly as we'd like, but racism has the tendency to feed on our efforts to accelerate the process.