I don't see abolishing legal marriage as such a big problem. I mean, yes, it is going to involve a lot of work to get it done, but when has creating equality for a group of people been easy or popular? I mean, its been over 40 years since the Civil Rights Act of 1964 was passed and there is still discrimination and racism in this country. Also, marriage wouldn't be prohibited and it wouldn't necessarily negate everyone who is already married. All it would do would be that a couple would have to apply for and receive their civil union at the courthouse, and then go to church and get married, or the other way around. I also disagree with the statement that abolishing marriage "skirts the real problem of discrimination against the gay community." You say that civil unions for everyone is the "equaling negation of them (civil rights)" I don't see how that is true. If you have two of the same exact water fountains sitting next to each other and one has a sign up by it that says "Whites only" and the other has a sign up that says "Colors only", if you take the signs down, how do you know which one is better?
The only way you can say that civil unions for everyone is some how a negative is by implying that legal marriage is in some way better than civil unions, which it wouldn't be because the only difference would be the name. This solution does not in any way reduce the value of marriage. It just seperates the contract of marriage, which would be a recognition by the church, and the contract of civil union, which would be a recognition by the state. You can have one or the other, or both if you want them.
This problem isn't going to be solved by waiting until everyone comes around and decides that being homosexual is okay. Sometimes the right thing isn't popular.