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You’re right to suppose that Schuon’s views on the subject of abortion were consistent with the teaching of traditional Islam as to the moment of quickening—a teaching shared by Saint Thomas, unless I’m mistaken—though of course they were framed in terms of the cosmologia perennis. According to Schuon,
“The individual substance, which ‘transmigrates’, is linked to the potentialities of the divine All-Possibility and has nothing to do with the genes that transmit hereditary dispositions; these dispositions are super-added to the substance of the individual and do not begin to be actualized until the moment the substance enters the body, more or less at the third month of growth; this combination constitutes the soul…. The birth of the soul takes place upon the entry of the individual substance—’transmigratory’, not genetic—whereas the birth of the body, the vehicle of the soul, is what is usually understood by the word ‘birth'” (Unpublished letter, Summer 1988).
A parallel observation comes as something of an aside in his “Mystery of the Bodhisattva”:
“The Enlightenment that occurred in the lifetime of Shakyamuni beneath the Bodhi tree is none other than what in more or less Western parlance would be called ‘Revelation’, namely, the reception of the Message or the prophetic function; just as the soul descends suddenly on the embryo once it is sufficiently formed—neither before nor after—so Enlightenment descends on the Bodhisattva who has acquired, side by side with his Knowledge and his Nirvāna, the cosmic perfections required for the prophetic radiation” (Treasures of Buddhism [World Wisdom, 1993], 124-25).
Needless to say, none of this meant that Schuon would have treated an as-yet-unensouled fetus with indifference. I’m reminded of the following:
“If a man does not trample on a flower without reason, it is because the flower is something of God, a distant effect of the infinite Cause; whoever despises a flower indirectly despises God. If a good man had the power to destroy a stone, he would nevertheless not do so without a motive, for the existence of the stone—this quasi-absolute something that distinguishes it from nothingness—is a manifestation of the Principle; it is therefore sacred. In every neutral contact with matter—and this is all the more true of contact with one’s fellow men—a man should either not leave any trace or else leave a beneficent trace; he should either enrich or pass unperceived. Even when there is a need to destroy—in which case the destruction is divinely willed—a man should destroy in conformity with the nature of the object, which then objectifies human nothingness to the extent the man is the agent of a celestial will. The life of man being sacred, the destructions it inevitably requires are also sacred” (Spiritual Perspectives and Human Facts [World Wisdom, 2007], 179-80).
Obviously, what is true for a stone is a fortiori true of a human embryo. I wouldn’t wish to opine as to how these considerations might apply to specific situations of the sort you mention—rape, incest, risks to the mother’s life, etc. What I will say is that there seems to be a spectrum of possibilities here and that one would be ill-advised in insisting that every abortion, no matter how early in the mother’s pregnancy and no matter the circumstances, should be regarded as absolutely intolerable.
We must be absolutists, of course, but ours is an operative and not, or at least not necessarily, a formulaic or propositional absolutism. It’s true that there can never be more than one perfectly appropriate act, but it’s impossible in every case to anticipate this act with a rule or a system of rules. Intrinsic or essential morality—the only morality that is never subject to conditions—is based on a discernment of principial realities and not on purely sentimental or pro domo considerations.