Well, your point is actually a logical inequality - apartheid was against the idea of interracial relationships, married or not.
It's not exactly like these interracial couples were offered a "union" which conferred the same rights, but don't call it a marriage.
But even if they were, it's still not close to the current battle over gay "marriage".
For most of recorded human history, the concept of marriage was very much tied to the idea of family.
For example, Susan Treggiari, a professor of Roman history writes "Matrimonium is an institution involving a mother, mater. The idea implicit in the word is that a man takes a woman in marriage, in matrimonium ducere, so that he may have children by her".
Homosexual relationships cannot by definition create a family - they are not a procreative relationship.
I'm not saying they're wrong because of this - this is simply a biological fact.
This is what a lot of gay marriage activists seem to miss - it's not opposition to the idea of them together. If they want to be together, they will be together.
It's simply that they wish to come along and redefine an existing word, to fit a new definition of what a family is.
Perhaps as a society, we will agree - and we will allow "marriage" between any two humans, and gender will become irrelevant.
However, to simply come along and assume, oh, a man and woman get it, so a man and man should get it automatically is either being intentionally blind, or very presumptuous.
A man and woman family is different to one composed of a man and a man - not because one is more valuable or not valuable - but simply because of their roles.
It's like saying, oh, a woman gets pregnant, so she must be more valuable than the man in a marriage. Well no, they are different - they play different parts, and we call them different things.