In 2E the Templars were clerics. The Templars were even better clerics than regular Dark Sun elemental Clerics due to major access to the sphere of Cosmos. The DS fluff about Templars is clear that Templar magic is different to arcane magic, and the Sorcerer Monarchs are not teaching their Templars anything, only turning on the divine magical spigot.
In terms of 3.5e, you shouldn’t even have this complaint. Templars cast from a fixed spell list and have domains. The domains differ between the Sorcerer Monarchs, so there is a slight difference between the Templars. My own version of Templar bring the Templar fully in line with the design philosophy behind Warmage and Dread Necromancer.
Templars are a cool and integral part of Athas. The game designers here at Athas dot org paired them down a little from their 2E cleric roots, and as much as I have disagreed in the past with some of their decisions, the direction that they took Templars in was good. I don’t see your complaint in relation to Templars holding water at all.
I don’t think that canon Athas presents as rife with arcane magic as you suggest. Yes there are many character options for arcane magic, including the special energy sources that has been discussed here recently. The solution isn’t a change in the canon, but at the table. I know that I would not allow an arcane spellcasting PC to preserve the mystery of magic in the setting. I’m sure you have your own solutions.