Back then (2003-2004ish), even some liberal/moderate/libertarian pro-gay people -- albeit usually straight people -- would echo your sentiment. They'd say:

"Let's just eliminate the federal government's role in marriage, and let all couples have access to civil unions."

That would have been fine with me, in theory. Unfortunately, I suspect the people advocating for such a solution weren't really reckoning with the reality that most heterosexual couples weren't going to respond well to the word "marriage" being removed from their legal recognition.

So, as you alluded to, the only options were really A.) full marriage as an option for same-sex and opposite-sex couples alike...or B.) same-sex civil unions with the exact same secular rights as heterosexual marriages outside of private entities and house-of-worship.

The truth is: A lot of this runaround from conservative folks was just a prolonged attempt to preserve the status quo of keeping same-sex couples as legal strangers. Fortunately, public sentiments have shifted to the point where even a plurality of conservatives are fine with same-sex marriage as long as it isn't imposed upon the private realms.