Why should historical discrimination matter to the policy? If at all, it should be about discrimination today.
Do you think their kids might be affected by say, the economic troubles their parents might've gone through, or the fact that they lost family due to the racial animus at the time? Or how about if those families were relegated to places designed specifically for them, to keep them away from the rest of the populace, with less opportunity for education or work. Do you not think that might have a multi-generational effect?
If Jews have had a hard time getting into Harvard in the past, and Harvard uses legacy status, then that means that Jews will.habe a harder time in the future for getting into Harvard.