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Let's use the context of marriage to illustrate the two types of discrimination here. What if I refuse to marry a person who is not Christian. Or, what if I won't marry a person who is not Korean? The first is discrimination based on religion, and the latter based on race. At first blush, the latter seems somewhat more nefarious than the first (Or maybe neither are nefarious at all). But why? Is race more fundamental to the person than his religion? I don't think so. It seems to me that one's religion (or lack thereof) defines a person as much as his race and ethnicity. (Well, that's my opinion. I guess it depends on each person and how they define themselves). Both concepts seem equally fundamental to our uniqueness as individuals and is why being discriminated against based on either you race or religion is offensive (or not). And our laws certainly treat them equally fundamental as violations against one's right to practice his religion and discrimination based on race are both afforded strict scrutiny, the highest standard of review by the courts.
Well, if the degree of fundamentality fails to explain the difference in the degree of negativity, than perhaps the answer lies in the results of such discrimination. For example, an employer refusing to give a job to a qualified candidate because he is black would certainly qualify as a nefarious result of racial discrimination. But if an employer refuses based on the qualified candidate's religious views, well, whats the difference? They both seem very troubling and a practice we should avoid. What about history? Does racial discrimination invoke visceral reactions because of our country's dark past with enslaving blacks? But religious persecution is the reason why our country was founded. Certainly our race troubles are more recent, but both types of discrimination/persecution have been central to our country's history. So I don't think history is a good explanation.
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Or is this endeavor simply fruitless? Because, let's think about it. Shouldn't we give FULL freedom to individuals so they can make rational choices for who they want as their life partner and who they want to populate the world with (Ok, boorish way to put it, but it's true folks)? Marriage is sacrosanct. And perhaps the sacro-sanctity makes marriage one of those exceptional circumstances that justifies discrimination. For instance, many Korean women who grow up and live in Korea may consider dating non-Koreans, but probably would not marry one. Koreans are a very homogeneous people. So it seems reasonable that Koreans want to marry fellow Koreans. And the same reasoning goes, I think, with not wanting to marry someone who does not share the same level of religious faith. You want to ensure that the strong tradition of faith is carried out through the lineage.
Ultimately, I think as long as you have a "good" reason for your exclusivity rule, it's more than justified, and therefore, completely rational. And is probably why we have not seen marriage lawsuits claiming racial or religious discrimination (at least from what I know) . I would hope, however, that rules are made to be broken.