Whose Autonomy is it anyway?

Marquette University rescinded its offer to Dr. Jodi O'Brien to be the new Dean of the arts and sciences. The Catholic University decided not to hire O'Brien because she is a practicing lesbian who has published articles on homosexuality.

Thomas Kozinski has a Mercatornet Article in which he discusses the dilemma this presents for Libertarians who place "Autonomy" as their bedrock principle:

"....Jodi O’Brien has the individual right not to be discriminated against by any institution with regard to her preferred sexual lifestyle, then it stands to reason that Marquette University has an institutional right of autonomy. Surely the individuals who govern Marquette have the right to govern in a way that conforms to their own preferences, even if that means discriminating in hiring criteria... if Marquette does not have this right, why does Jodi O’Brien retain hers?"

In other words, the principle of Autonomy cannot resolve the 'conflict of wills.' If the individual will is sovereign, then how do we adjudicate disputes between them? Should we side with Marquette's President, Fr. Wild, who has a right to hire whomever he wants or Dr. Brien who has a right not be discriminated against? A principle other than Autonomy has to be invoked in order to resolve the conflict.