Because for starters, the Garleans still have their normal sight.
As for the magic. I think the Garleans cannot use Aether like the other races because they do not have as much aether as the other races. They know how it works and how to artificlay produce it to power their machines, but they do not have enought for even a simple teleport spell
Thancred's case is similar, the trip thought the Lifesteam did drain him of all his aether to the point where he has as much as a Garlean and it is unlikely that he'll even regain that lost aether again.
Also I think Minfilia might have sabotaged the spell, causing it to spare Y'sholta's aether but take away her sight as the "toll" through the lifesteam.