Discrimination is generally considered bad because it is, for lack of a better word, unfair. As a result, people often slam affirmative-action programs because they feel that they try to compensate for unfairness in society by reverse unfairness, which is ... unfair.
Mind you, if there really is still persistent unfairness in hiring, then legislated reverse unfairness would only even the scales. But if there isn't, then reverse unfairness would produce an unfair situation.
As for his quotes:
Meritocracy is no more than an ideal that the public is at liberty to embrace, not a right belonging to each potential job applicant that is a constraint of justice on public policymaking.
That is correct. Meritocracy is a social ideal, not a "right". Nowhere is meritocracy enshrined as a right.
Discrimination becomes morally invidious only when it either (a) expresses hatred, contempt, or the like against those who are excluded or (b) has a serious negative impact on the life prospeects of those excluded
By that definition, discrimination against mentally retarded people is immoral because it significantly affects their lives. That's why the "unfairness" criterion is more widely accepted.