Nobody has a RIGHT to federal funds. They have rights to life, liberty, and the pursuit to happiness, but they don't have a right to put their hands in the till.
It seems to me that that is the basic issue.
I don't see how they win this case. Gays are not a protected class in this country. Unless they start making up some equal protection garbage (which has been liberal courts' modus operandi for ages now), I don't see what grounds they have.
How are they going First Amendment on this one? Their freedom of speech is one thing, but having the government thrown off the premises because it does not Havard's own system of governance AND THEN demanding that funding should continue pushes this into some nebulous law-law ;) land.