Ends do not justify means.
It is never permissible to do evil so that good may come about: "let us not do evil that there may come good" (Rom. 3:8). Sin sometimes must be tolerated in order to prevent a greater evil.
St. Thomas Aquinas's answer to the question of "Whether the rites of unbelievers ought to be tolerated?" (Summa Theologica II-II q. 10 a. 11 co.) could be applied, mutatis mutandis, to whether abortionists ought to be tolerated:
although God is all-powerful and supremely good, nevertheless He allows certain evils to take place in the universe, which He might prevent, lest, without them, greater goods might be forfeited, or greater evils ensue. Accordingly in human government also, those who are in authority, rightly tolerate certain evils, lest certain goods be lost, or certain greater evils be incurred: thus Augustine says (De Ordine ii, 4): "If you do away with harlots [or abortionists], the world will be convulsed with lust."
cf. Vermeersch, S.J.'s ToleranceTolerance
In "Whether human law should repress all vices?" (Summa Theologica I-II q. 96 a. 2 co.), St. Thomas shows that human law should forbid murder:
human law is framed for a number of human beings, the majority of whom are not perfect in virtue. Wherefore human laws do not forbid all vices, from which the virtuous abstain, but only the more grievous vices, from which it is possible for the majority to abstain; and chiefly those that are to the hurt of others, without the prohibition of which human society could not be maintained: thus human law prohibits murder, theft and such like.
Thus, "laws" permitting murder are no laws at all.
Abortion a state of war?
If the millions of abortions happening yearly constitute a state of war, then just war theory might be applicable. "In order for a war to be just, three things are necessary" (Summa Theologica II-II q. 40 a. 1 co.):
"the authority of the sovereign by whose command the war is to be waged"
"a just cause is required, namely that those who are attacked [e.g., abortionists], should be attacked because they deserve it on account of some fault [e.g., killing innocent babies]."
"it is necessary that the belligerents [e.g., anti-abortionists] should have a rightful intention, so that they intend the advancement of good, or the avoidance of evil [e.g., ending abortion]."
Conditions #2 and #3 certainly could apply to abortion, but it is unclear that condition #1 applies. Has any civil ruler ever openly declared war against abortion?