It seems to me that discrimination, as the word is currently used in America, at least, is a legal category involving the infringement of people's rights or the withholding of their opportunities based solely upon either integral characteristics (skin color, ethnicity, gender, age, sexual orientation) or upon those matters of personal choice which we have declared constitutionally protected, such as religion or political affiliation.
There is also a difference between discrimination (which is an action) and prejudice (which are opinions). America's a free country: you can be an asshole if you want to. If I were a racist, for example, there's nothing preventing me from joining some creepy group of white fascists to sit around and call people names and trade racist jokes and stuff. But as soon as I don't hire someone at my business because he's a Jew, or I have security follow him around my store because he's black, that's discrimination.
Preference, by comparison, is not prejudice (which is a baseless hatred), nor is it an action like discrimination. My preference is not to eat cucumbers. The reason for this is that I do not enjoy the taste or texture of cucumber. I don't care if others eat them, and if you love them, I will not think less of you. Also, on certain social occasions, when I have been served cucumber, and it would have been quite rude to refuse it, I have eaten it, and have not resented the fact.
To put it another way, if I am faced with hiring an assistant, and my choices have come down to two candidates, both of whom are women of roughly equal experience and ability, if one is Indian-American and one is Irish-American, and I hire the Irish-American one because she's white and I don't like immigrants, that is discrimination. On the other hand, if one is outgoing, pretty, and witty, but the other is morose, plain, and dull, and I choose the first one because she'd be more fun to work with, that's preference.
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Dull sublunary lovers love,
Whose soul is sense, cannot admit
Absence, because it doth remove
That thing which elemented it.
(From "A Valediction: Forbidding Mourning" by John Donne)
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