St. Thomas Aquinas wrote that life does not begin until the second trimester. How should we answer this, especially in regard to abortion?

The wording of your question is slightly inaccurate. St. Thomas did not deny that life in the womb was, in fact, life. The teaching of Aquinas to which you refer is that an unborn baby receives a soul 40 or 80 days after conception, depending on gender. (Note this is much earlier than the second trimester). Aquinas held this opinion based on Aristotle, who said a child has a soul when it first has a human “form"--that is, when the child looks human. The difference in gender was based on the point at which genitals could be observed on miscarried children, earlier for boys, later for girls.
 
While many link this position of Aquinas to the abortion debate, the date of ensoulment is not essential to the Church’s position on the sinfulness of abortion. The Church roots her teaching in Scripture (e.g. Ex 21:22-23; Ps 51:5; Ps. 139:13-16; Job 10:11; Is 44:24; Jer 1:5), Tradition and Natural Law.
 
St. Thomas never wrote directly on abortion. There are only a couple of indirect references in the Summa (IIa, IIae, q.64, a 8; q.68, a 11). But surely St. Thomas was well aware of the Scriptures above, as well as the ancient teaching of Tradition forbidding abortion at any stage. Beginning with the Didache written around 110 AD which said "Thou shalt not murder a child by abortion" (2:2), and continuing with Barnabas, Clement, Tertullian, Hippolytus, Basil, Chrysostom, Ambrose, Jerome and many other Fathers, and also authoritative Councils, the Church had consistently condemned abortion in no uncertain terms. Hence we ought not presume Aquinas, who never spoke on abortion directly, ever intended by engaging in a discussion of ensoulment, to contest the immorality of abortion at any stage.
 
Regarding his teaching on ensoulment, theologians do not hold such an opinion today and most regard Thomas’ positions as rooted in a primitive understanding of embryology. Clearly natural science today demonstrates the existence of a genetically unique individual at conception.
 
Finally, even if one wanted unreasonably to hold that Aquinas supported early abortions, St. Thomas, venerable and respect though he is, is not infallible and is not the magisterium. While his teachings are influential, they have not been universally adopted by the magisterium. One obvious example is that St. Thomas was not supportive of the, then unofficial, belief in the Immaculate Conception of Mary.