If an additional 1000 2.0 students applied to Harvard next year this number would look even worse. But would the change be meaningful?
That's not to say they don't take legacy into account. But, as presented, those numbers can be misleading.
Similarly, if you're trying to have a successful interview with a company, it helps to talk to people who have interviewed there before, preferably people who have interviewed there successfully.
(The process may well have other issues that make "legacy" applications more likely, but a higher acceptance rate of such applications doesn't inherently suggest a problem.)
Legacy applicants are X% more qualified naturally (well educated parents, etc), and get Y% from the admissions. Given the numbers for Harvard, MIT, etc, there are plenty of qualified applicants for each spot.
It seems more likely that in the applicant pool the non-legacy kids would be smarter. Imagine how confident of your ability you'd have to be to apply to Harvard as a random kid from a public high school in Iowa. Whereas if you'd grown up expecting to go there because your parents did, the threshold for applying would be pretty low.