The distortion here is bizzare. It is the CLS (Christian Legal Society) who want to exclude others on impermissible grounds, not the other way around. And as a matter of fact, CLS is perfectly free to discriminate as long as it doesn't insist on using school's money. The issue arose because CLS wants an "official recognition" of the school, which is an alias of the government sanction in this case.
The school has a non-discrimination policy that reads like any other: on the basis of race, national origin, religion, sex, sexual orientation, age, etc. Of course it is easier to target gays in today's legal environment, and I believe this is part of the long running campaign of the religious right who precedes their political gain over anything.
Indeed, CLS had no problem with gay members in the past. The policy change came from 'up above' recently. This isn't an isolated incidence in this area - Boyscout in NJ, adoption center in MA, and now schools in CA; Local Boyscout had no problem with gay scoutmaster, let alone gay members but its national committee suddenly pressures to lose them. A local Catholic adoption center always welcomed same-sex couples but suddenly changes its policy after same-sex marriage becomes legal (no doubt because the church remembered its forgotten 'teachings'), Christian students organization that used to embrace gay Christian students shuts its door after the national leadership decides on a new crusade against gays.
There are, of course, legal issues on each case but there is also an unmistakable theme in all of this, which is the desire of the religious right to prevail in public sphere. And unfortunately it takes a bigoted idea more often than not - it is easier targeting real people than targeting some abstract sin, which obviously isn't enforceable.
It wasn't too long ago when a religious school had an official policy of banning interracial marriage.
Bob Jones University v. United States. (A fun quote: The ban on interracial dating was lifted in 2000 after Dr. Bob Jones III, following a media uproar prompted by the visit of presidential candidate George W. Bush, announced its nullification on Larry King Live) Think about it.