I think it's because Ki attacks have something to do about drawing power from nature, or from THEIR OWN SPIRIT ENERGY.
The problem is that in franchises where Ki attacks are introduced, spirit force is separate from life force. That is not the case in Index, as the spirit force (mana) needed to cast spells
are derived from the magician's life force and a small fraction of energy from nature.
I would say that Ki attacks could be construed as Gemstone esper abilities developed OUTSIDE Academy City since
it's not drawn from the user's life force. Flat What.
And to be fair, there shouldn't be a lot of people who do Ki attacks in Index considering that there are only 50 Gemstone espers in the world.
Of course, another way around it is to theorize that Ki attack users
draw most of their powers FROM NATURAL ENERGY plus a small fraction of their life force.
So, yeah, Ki attackers are
mages. It's just that Ki attacks are NOT runic magic, but rather a different kind of Functional Magic honed by integrating oneself to nature.