Maybe it's a matter of definition -- and I'm not sure the game text itself is 100-percent consistent in this regard -- but I think there are some distinct categories that sometimes get blurred here.
Essence: a kind of life-force, mana, "the Force." An all-pervasive but subtle and immaterial aether that exists at the root of ALL being (like the Hindu concept of Brahma), though it may not be perceived by the non-enlightened, and the ability to manipulate it is the special province of the initiated adept.
Magic: the broad discipline of using the power of mind ("Intelligence") to channel and focus Essence in order to accomplish specific tasks. Grouped in general categories -- Healing, Blessing, Battle, Mental -- magic seems to be regarded in the Geneforge universe as morally neutral, capable of being used for good or ill.
Shaping: a form of genetic engineering. It is closely analogous, but not identical, to the "hard science" version of GE that exists in our world (in which genes are physically manipulated in order to create novel life forms). This is shown by such things as shaping "tools" and "laboratories," and those quasi-scientific devices in GF2 that you could peer into and see tiny objects that sound a lot like chromosomes. Yet the version of GE that exists in the Geneforge universe seems more closely akin to magic (as defined above), in that it appears to involve a focusing or channeling of essence, not physical genes.
Shaping could, in this view, be regarded as a kind of offshoot or discipline -- or heretical deviation, if you prefer -- of magic in general. Or it could be regarded as a kind of parallel tradition, like the different kinds of Yoga identified by Shiva in the Bhagavad Gita, each of which is valid and powerful, all of which draw upon the same universal essence or Brahma, but each of which also is quite distinct.
On this basis, I think you could legitimately take a position that is opposed to Shaping, specifically, but not to magic in general. One might even argue that magic is too diffuse, manifold and ubiquitous to oppose -- that it is an innate power of consciousness, human and non-human. One may object to specific magical operations or "spells," such as Aura of Flames, yet not to others like Heal. (The Geneforge universe seems to recognize such distinctions, as in the high-level spells of GF2 that could not be learned unless the character is "changed.")
But for all this, I think the game text is somewhat blurry. For instance the term "shaper" is used in earlier games to refer to ANY character, whether or not he or she has learned or utilized any shaping abilities. Elsewhere, however, there is a clear and consistent line drawn, i.e. "Teach me magic" as opposed to "Teach me shaping."
I'm only halfway through GF4, but I'm feeling some Trakovite sympathies. And in that sense I agree with the sentiment of the topic title, because I do think this makes me suspiciously "unshaperlike."