After all, traditional marriage isn't just analogous to sex discrimination—it is sex discrimination: Only men may marry women, and only women may marry men. Same-sex marriage would transform an institution that currently defines two distinctive sex roles—husband and wife—by replacing those different halves with one sex-neutral role—spouse. Sure, we could call two married men "husbands" and two married women "wives," but the specific role for each sex that now defines marriage would be lost. Widespread opposition to same-sex marriage might reflect a desire to hang on to these distinctive sex roles rather than vicious anti-gay bigotry.
Mormons are invested in gender. In fact, gender is eternal. The priesthood applies only to males. Women are excluded from almost all leadership positions in the Church. Men preside in the home or do so at least ceremonially. If 'husband' and 'wife' are not necessarily distinct roles then why should women put up with the current system? Hmm... maybe gay marriage does upset the apple cart, after all.
I'm for federally recognized civil unions as an intermediate step along the way toward full marriage equality. For now, let's just avoid the quagmire of unresolved gender-role issues that seems to have the rest of America knee deep in muck. Federally recognized civil unions would give us desperately needed rights (like not having your non-US boyfriend deported). Maybe it's true that a civil union is 3/5ths of a marriage, but right now excuse me for not being so picky.
Civil unions that are recognized only at the state level are probably 1/5th of a marriage, if that. Also, marriages that are not recognized by the Federal government are of significantly protective value than other marriages. If forced to choose, I'd take a federally recognized civil union over a marriage recognized only at the state level.