Those who believe in freedom, don't care for government enforced discrimination (whether during slavery, Jim Crow, or affirmative action). But they do support (like free speech) the freedom to associate or not (which is in the 1st amendment), which means that a Jewish/black hotel owner could turn away KKK for a convention in their hotel. But it also means people might stupidly discriminate on things other than merit.
Your post confuses nepotism with discrimination. And it confuses the freedom of private institutions (like Harvard) to discriminate for their own reasons, one being that giving some degree of preference to children of alumni might result in more donated cash from the alumni.