Fortunately, the very question was treated in the supplemental to Summa Theologicae III, so with a little care we can see what the Thomists thought was the right answer. It's a subtle point, and a problematic one, as we'll see.
Dr. Althouse's objection is actually the very first objection the Summa treats. She puts it this way:
It's not as though marriage exists in nature. Marriage is an "arbitrary boundary created by man." The only boundary in nature is between having sex or not. Nature puts up no boundaries about when or with who (or what) any given animal has sex. Nonprocreativity doesn't set up a boundary.That's not right, the scholastics argued, because "nature" means more than one thing. You only come to that error by equivocating between the meanings.
Man's nature inclines to a thing in two ways. In one way, because that thing is becoming to the generic nature, and this is common to all animals; in another way because it is becoming to the nature of the difference, whereby the human species in so far as it is rational overflows the genus; such is an act of prudence or temperance. And just as the generic nature, though one in all animals, yet is not in all in the same way, so neither does it incline in the same way in all, but in a way befitting each one. Accordingly man's nature inclines to matrimony on the part of the difference, as regards the second reason given above; wherefore the Philosopher (Ethic. viii, 11,12; Polit. i) gives this reason in men over other animals; but as regards the first reason it inclines on the part of the genus; wherefore he says that the begetting of offspring is common to all animals. Yet nature does not incline thereto in the same way in all animals; since there are animals whose offspring are able to seek food immediately after birth, or are sufficiently fed by their mother; and in these there is no tie between male and female; whereas in those whose offspring needs the support of both parents, although for a short time, there is a certain tie, as may be seen in certain birds. In man, however, since the child needs the parents' care for a long time, there is a very great tie between male and female, to which tie even the generic nature inclines.The language is a little archaic even in translation, but it can be simplified. "Nature" isn't a simple synonym for "bestial," and making human beings more like beasts was certainly never the Church's point.
Now, there are some ways in which human beings are like other animals, so that (for example) it would be a violation of natural law to pass a law requiring people to forgo food or water. But there are other ways in which human beings are different from other animals, especially in that we naturally have a larger access to reason. One of the things we can reason about is the fact that, also by our nature, male and female produce a child who requires a long upbringing and education. Thus, we can reason that the perfection of our sexual nature is in the successful rearing of the child, which requires a strong union between the parents. This is the institution of marriage, which is therefore of human nature.
If you want another institution that points to a different need, that's fine: humans are also political by nature (a point made in the same article). As we've discussed before, Aristotelian friendship looks a lot like what 'same-sex marriage' advocates really want: unity of property and concern between (usually) two people, to pursue each other's good in a sort of loving friendship. That could have a sexual component or not -- certainly the Greeks would not have been troubled if it did.
It's distinct from the natural law marriage, though, which comes from this reality about how we produce offspring, and what the needs of those offspring are.
There are two points worth thinking about, though:
1) I think the sed contra is confusing on this point: "Further, the Philosopher (Ethic. viii, 12) says that "man is an animal more inclined by nature to connubial than political society." But "man is naturally a political and gregarious animal," as the same author asserts (Polit. i, 2). Therefore he is naturally inclined to connubial union, and thus the conjugal union or matrimony is natural."
Aristotle clearly thinks that the political union is the more natural because it is only in a political union that human beings can fully achieve their rational potential. So the point being made here is not that marriage is more natural than politics, but only that it is natural since we are inclined to it even more than we (naturally) are to politics.
2) The family nevertheless has a kind of independent status under this reading. It's pre-political. It is (Politics I) different in kind from the state, and Aristotle rejects Plato's idea from the Republic that families should be structured by the state for its own purposes. It's one thing that the political should not intrude upon. Aristotle's clear assumption is that the political union is made up of pre-existing families. These families can unify in friendship in other ways too, as for example in a unity of the sort described above as "Aristotelian friendship." In terms of politics, though, the role of politics is to provide a kind of security among non-family members. It's assumed that you will treat your own kin with favoritism, and in order for a political union to be stable that tendency has to be resisted. So, for example, a single family should not dominate the leadership of a country or a political faction: but of course a father will care more about his son than a stranger.
Where our current debate is most dangerous, it strikes me, is in destroying that natural independence of the family and bringing everything under the rule of the state. That's the gravest danger in this debate: not that some men will go off and do whatever they were going to do anyway, somewhat more easily than before, but that the natural love of parents and children shall be ever more tightly bound by the intrusion of the political and the state. That was Plato's ideal for his guardians, but it is an impossibly tyrannical scheme. Just because it is such a violation of human nature, no state could pursue it and remain legitimate.
That is what must be resisted above all.


