This is just my personal view on the subject, and it's not strictly canonical. One of the key attractions of the arcanist class for me has always been the "dual" nature of its abilities.
As you said, the arcanists of Limsa Lominsa are more akin to scientists and mathematicians (which is why it's not really correct to describe their role as "sacred"; that would be a more apt description for the thaumaturges of Ul'dah or the conjurers of Gridania).
And the key point about science is that it's inherently neutral. It's just a tool. It can be used to harm just as easily as it can be used to heal. In this sense, it's very similar to alchemy, which can be used to create both medicines and poisons.
Others in this thread have pointed to the elemental nature of both conjury and thaumaturgy. Arcanima, in contrast, is non-elemental, because it's all about using arcane geometry to manipulate the aether within bodies and objects. If you like, you could think of it as arcane "physics". Unlike conjury or thaumaturgy, which deal primarily with ephemeral forces, arcanima is all about dealing with actual physical objects.
So, a formula that causes aether to knit together bodily wounds could easily be reversed to tear apart flesh and bone. (Think, for example, of real-life thermodynamics: the application of heat causes objects to expand, but the removal of heat causes the reverse).
Such manipulation of aether lies at the very heart of arcanima. An arcanist is someone who applies magic to both maim or mend, and the jobs that branch from this vocation — summoner and scholar — are in effect, two sides of the same coin.
In principle, this is very different from thaumaturgy, which evolved from funeral rites for breaking down corpses for burial (ie, it's inherently about destruction), and conjury, which is about borrowing the power of elementals to preserve natural harmony.



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