This is a near perfect example of the need to limit government to the things that it is absolutely necessary to be involved in. The essential question is what is a 225 year old secular government doing trying to define a Religious Sacrament Marriage is a Sacred Religious Covenant that has been around for more than 5,000 years and it should have stayed that way. Instead someone got the bright idea to let The State butt it's nose into it not because it was necessary but because they didn't see where it would do any harm because at the time the idea of Same-sex Marriage would have seemed absolutely preposterous.
So now we're stuck in an untenable position, on the one hand you have the Religious community who see's those pushing for S/S Marriage as people who have no respect for their Sacred Religious beliefs trying to make them update this 5,000+ year old tradition for nothing more than modern Political Correctness.
On the other hand you have the Gay Community who feel they are being discriminated against by a group of narrow minded Religious bigots. If Marriage had been left alone as a Religious Covenant this would never have been an issue but since the Government got involved there are all kinds of legal issues. We've all heard the issues, inheritance, medical visitation and decision making and so on and the Gay community feels they are treated as second class citizens, as though their relationships, their feelings were any less genuine than those of Heterosexuals. And they are right to feel that way.
I'm a Born Again, Evangelical Christian and I would have a serious problem if my Pastor started performing Same-Sex Marriages but by the same token I am an American and it is far worse for my government to treat a Homosexual couple as though they were less than a Heterosexual couple in the eyes of the law.
The OP asked why "gays" can't accept Civil Unions and just be done with it? The simple answer is because no one is suggesting that Heterosexuals should have to so why should they. If the 9 people on the SCOTUS really wanted to put this to rest they could simply step back and say that from now on no government body shall perform Marriage ceremonies, only Civil Unions. If a couple wanted to be Married they go to a church and to simplify matters Pastors, Priests, Ministers and the like would be able to incorporate the Civil Union ceremony into the Marriage ceremony so that if a couple is Married in a church they are also joined in a legal Civil Union.
The Marriage ceremony would be strictly for Religious purposes and the Civil Union would cover legal matters. This would put Heterosexual and Homosexual couples on equal footing in the eyes of the law, no difference in their legal rights. I don't know of any Homosexual couples who are fighting for the right to be married in a church, they just want to be equal in the eyes of the law and I don't know of any Heterosexuals who care if Homosexual couples are given legal rights on par with their own it's only the tradition of the Religious Sacrament of Marriage and millenia of understanding what it meant that they didn't want changed based on the standards of the day