The medical analogy is in good one, but you fail to follow it through to it natural conclusion.

Of course we care about the side effects of our medicine! This is an absolutely basic concern. Sometimes the side-effects are worth it because the disease is worse, but pharmaceutical companies spend billions and billions of dollars trying to find drugs with better side-effect profiles specifically because they, and we, are very well aware of the reality that the side-effect is caused by the medicine not the disease! For example, chemotherapy drugs are absolutely awful not because cancer is awful but because they are poison. They are horrible for you and have terrible side-effects--but they're even worse for the cancer than for you, so people take them anyway when there's a good chance they'll cause remission of the cancer. But people are constantly searching for better alternatives because all the hair loss and nausea and everything--that's NOT cancer, that's all side-effect!

If affirmative action causes insecurity because by its nature it is absolutely true that you could be selected because your skills are worse but you are the right race then we have to ask ourselves: is the side-effect worth it? And the answer may well be not just yes, but absolutely yes: the loss in pride, and triggering of imposter syndrome when you actually were the best, is well worth the placement of a more diverse and lesser-but-still-adequately-skilled set of people into these positions. Or the answer may be no: in fact, the side-effects of the medicine are not worth it. Or the answer might be: we would take this medicine if we had nothing better, but in this case we do have something better so we should shift to that instead.

The idea that we should be blind to the side-effects of treatments is simply not supportable. That this is true is more obvious if you propose treatments that help the disease but have more serious side-effects. For instance, you can quickly achieve racial equity in representation in a particular company or field by immediately firing people of the overrepresented races and hiring them from the underrepresented races, no matter how qualified (take the best there is and worry about on-the-job training later). This medicine absolutely cures that aspect of the disease, but the side-effects are immense, because of the massive loss of expertise and replacement by lots of people who haven't had adequate training to do the job.

In contrast, affirmative action is better medicine, even though it doesn't treat the symptoms as quickly, because the side-effects are far less. But we should always be seeking better medicine which either treats the disease more completely or has reduced side-effects or both.

For instance, Harlem Childen's Zone takes the legacy of racism and poverty and says: right, we're intervening early--we're not giving up on these kids, we're believing in them and helping them succeed. By the time they graduate, they're far less disadvantaged by the ongoing impact of racism than they would have been if they'd gone to some poorly-funded school where nobody cared about them. The medicine is expensive, but there are approximately no side effects at all. It's all a win (save the expense).

If you present to me two options: one, HCZ, or two, schools are garbage but we use affirmative action to get the same fraction of graduates into college anyway, the medicine I would take is HCZ.

Yes, it's more expensive. But no side effects! You just give people the education they need to have a better shot at a more satisfying life: the shot they always should have had anyway.

So, mind the side-effects. Of course, if you get an opportunity that works for you, take it! If it was for objectively bad reasons, well, that's on them: if it's good for you, take it! But advocate for the best medicine and keep trying to find it. Don't pretend the side-effects don't exist just because a medicine is helping with the disease.