We can sit there all day quibbling about terms, but I am unconvinced that piercing the eyes would suffice to end Lahabrea, when being absorbed into a Primal did not suffice to do the job by that point. It's no blade of light piercing him - and again, it would not suffice to destroy him, just to expel him to the Aetherial Sea, assuming it worked. Meanwhile, Emet was struck with that, and as she notes, "believed" to be completely destroyed.

Our boy's coming back.