If two people have the exact same accomplishments, except one is from sex/race subjected to discrimination, then isn't there a good chance that the disadvantaged person would have done more if not subjected to said disadvantage?
Is there a chance? Of course there is.
Is there a good chance? I'm not convinced that there is. A person's life is a complex thing, and the advantages and disadvantages we face interact in extremely complex and sometimes completely counterintuitive ways. For one candidate, things may very well work out as you say: without the disadvantage, the character could do better. Another candidate may use the relative freedom from disadvantage in other ways, unrelated to the task at hand, resulting in a candidate who is very different from the one in question, but not particularly better or worse. There is a third possibility: you seem to imply that those who actually don't face these sorts of disadvantages essentially rest on their laurels, but if they do, then we must also entertain the possibility that a currently-disadvantaged candidate, if he or she were not to have faced these disadvantages, may have done the same, resulting in a candidate who is once again not particularly better, and perhaps even worse.
There is no way to predict what a candidate might have done if they had not faced disadvantages. Because of this, the question has no meaning, and should not be considered in hiring decisions. We must act based on what is in front of us, not on what might have been.
Doesn't that in fact make the disadvantaged person the "better" candidate?
It might, in a parallel timeline where the disadvantage did not in fact apply. But we cannot gamble on parallel timelines; we can only go by what is real, in history as we know it. And by that history, you have two equal candidates.