You could make the same argument for why any kind of prejudice should be allowed since, for example, racism provides an advantage that functions in the real world. This seems like a bad defence for legacy admissions.
There are hundreds of colleges, many of which have high acceptance rates and perfectly fine instruction. Are these applicants or the people in this thread then displaying preference or prejudice in the institutions they apply? And if so, what makes it different than the institutions do the same?