More or less. Imagine you're Garlean leadership for a moment. You've heard tales of this sacred place and know there are tons of legends about it. You find that it is a conflux for
at least the whole realm (if not the whole
world)'s aetherial rivers.
If your empire's mission statement is essentially
Primals Are Bad, M'kay, you definitely want that place locked down when your armies move in. The last thing you need is the beast tribes tapping into that
massive confluence to power the summoning of their gods.
No one can be allowed to learn how to harness that power.
That's not to say that the Garleans didn't realize something
bigger was up with Silvertear Lake, though... especially while pulling away from the Battle of Silvertear Skies.
Fun Fact: Even after the invasion into the heart of Eorzea failed and the XIVth Legion retreated to Ala Mhigo, Gaius
still held Mor Dhona (very loosely). Eorzea secured small camps around the aetherytes, but barely anyone
dared venture outside of them because Gaius maintained supply camps and a troop presence. That's how Castrum Novum was raised there so fast with so few noticing.