That didn’t save Bob Jones University from federal intervention. If they can punish a school for practicing radical discrimination, they can punish a school for discriminating against gays.
If a religious institution claims that it is an important part of their belief system that they be able to quietly pray in private, then any government that denied them the ability to do so would rightly be declared tyrannical and guilty of persecution.
If a religious institution claims that they need to engage in human sacrifice of unwilling victims then a government that prevented them from doing so would be considered sane.
The Bob Jones Univ case is one of those borderline cases. Our Constitution has been interpreted to make racial discrimination a crime. Some may argue that that is an incorrect interpretation of our Constitution, but there it is. Under the current generally accepted interpretation Bob Jones Univ was engaging in discrimanatory behavior which the federal government had an obligation to stop. I'm not exactly certain of the particulars. If Bob Jones University had a single student in attendance receiving federal loans, then they would be considered as an institution receiving federal aid and would come under the jurisdiction of all of the appropriate federal laws. This is why places like Hillsdale refuse all federal aid.
If at some point in the future discrimination against gays is put on a par with racial discrimination then the federal government will be required to oppose it regardless of whether a particular institution is getting federal funding. This is the point at which the government would begin persecution.
There would presumably still be a significant number of citizens around who would, for example, oppose gay weddings performed on their premises. If they attempted to prevent such weddings from proceeding and the government tried to stop them then all hell should break lose.
But I wouldn't hold my breath.