The chief reason for opposition to the civil union bill is an underlying belief that homosexuality is wrong. The two most common justifications given for this belief are that a) homosexuality is "unnatural", or b) that God (through the Bible) says it is wrong. However, both of these attempts at justification fail to provide an ethical basis for the conclusion that homosexuality is wrong (or any other ethical conclusion, for that matter).
The view that homosexuality is "unnatural" runs into an immediate problem if applied literally, in that it is simply mistaken about the "natural order" it claims to look to for moral guidence. Homosexual behaviour is widespread in the animal kingdom, and humans seem to be unexceptional in that regard. Shifting to a telelogical claim that "the purpose of sex is reproduction" and that something is immoral if it does not serve its purpose suffers from the same flaw, as it seems that in nature sex is not used solely for reproduction. Bonobos, our second-closest primate relatives, use sex as a greeting, as a form of bonding, and during food sharing (in fact, according to Frans de Waal, "anything, not just food, that arouses the interest of more than one bonobo at a time tends to result in sexual contact. If two bonobos approach a cardboard box thrown into their enclosure, they will briefly mount each other before playing with the box"). In humans, sex seems to be used most frequently for pair-bonding. A further shift could be made to claiming that the purpose of an organism is to propagate its genes (and that homosexuality is therefore wrong as it interferes with this), but this completely ignores the fact that homosexuals frequqently do have children - and that many hetereosexuals do not (that's quite apart from objections based on the vehicle / replicator split, or from the liberal pluralist position that the only "purpose" for a person is that which they define for themselves).
But there's also a more general problem with this claim, and that is that it purports to derive a moral conclusion (an "ought" statement) from facts about the world ("is" statements). But David Hume pointed out long ago that this is troublesome:
In every system of morality, which I have hitherto met with, I have always remark'd, that the author proceeds for some time in the ordinary way of reasoning, and establishes the being of a God, or makes observations concerning human affairs; when of a sudden I am surpriz'd to find, that instead of the usual copulations of propositions, is, and is not, I meet with no proposition that is not connected with an ought, or an ought not. This change is imperceptible; but is, however, of the last consequence. For as this ought, or ought not, expresses some new relation or affirmation, 'tis necessary that it should be observ'd and explain'd; and at the same time that a reason should be given, for what seems altogether inconceivable, how this new relation can be a deduction from others, which are entirely different from it.
What Hume is saying (in his eighteenth-century English) is that there can be nothing in the conclusion which is not already in the premises; if all you have are "is" statements, you can't derive an "ought". In practice, this means that any argument from nature needs an explicit linking premise to provide the moral content. The most common linking premise is a simple definition: natural = good, and unnatural = bad. The problem is that this immediately founders on the fact that nature is red in tooth and claw; rape and murder are both natural, as is cannibalism (just look at all those animals where the male eats any unrelated offspring), but we don't want to regard any of those as being good. The second most common link is to invoke god, which is dealt with below.
What about the argument that homosexuality (or anything "unnatural") is wrong because God (through the Bible) says so? This is known as the Divine Command Theory of ethics, and its flaws can be seen the moment you pause to think. If things are wrong solely because God says so, morality is essentially arbitrary, a game of divine "Simon says" only with the possibility that rape, torture and murder would actually be good if God decided that they were. We're left with the "morality" seen in Genesis 22:2 (in parody: God commanded Abraham to sacrifice his only son, and it was good). What's being promoted here is not morality, but blind obediance to authority - something that is very definitely not good.
(The Divine Command Theory also reduces claims that God is good to a vacuous tautology - God is good only in the sense that he does whatever he wants to. Four-year-olds do whatever they want to too; does that make them good?)
Neither of these common arguments provides a proper basis for believing that homosexuality is wrong. If opponents of civil unions wish to rely on a moral argument against homosexuality, then they will have to look elsewhere for justification.