In my opinion, the civil union part of marriage is the legal benefits while the marriage is the spiritual or cultural part. Therefore, the government shouldn't concern themselves with marriage, only civil unions. And for a stepping stone to marriage, it definitely is. While it isn't enough (so long as we don't fully adopt civil unions), it's a first step.
Progress, like most things in life, is a process. On the whole, people who believe homosexuality is a sin would probably be more tolerant of civil unions than of marriage. Allowing civil unions allows those people to get comfortable with the idea of civil unions. Once that happens, the next step to marriage becomes easier for them to accept, rather than making the jump all at once. It sucks that change caters to how comfortable the people resisting it are, but that is the way it works.
Civil unions can create opportunities for rights in the future by starting a couple in the right track with state benefits. However the amount of rights is so severly limited that it makes civil unions slightly obsolete these days. A couple cannot use their rights from state to state, which would hinder their situations if they needed to move somewhere else. It also creates a situation where if 2 decided to divorce, they would be unable to.