It sounds like you don't really know if they are being discriminated against, even though you are stating it as fact. The 3% number could be biased due to any number of reasons, conservatives may not apply to Harvard for ideological reasons, or student ideologies may shift during education.

It's possible that you can identify right-wing high schoolers based on their writing, but I don't really see a problem with rejecting students if they are touting unpopular and/or discriminatory ideas. Universities have the right to maintain a culture of openness and learning, and conservatism is often antithetical to that.