Unless Y'shtola can train others to use her aethersight, no, the alliance will not be able to rely on that method to scan their forces for tempered intruders. For now, the alliance is no closer to detecting such spies than they ever were, and will need to continue to use old-fashioned OPSEC to prevent sabotage. Assuming that Y'shtola CAN train others to do it, it's possible that in the future the Alliance might gain a powerful tool to use against Primal infiltration - however, for ethical reasons, Y'shtola may be reluctant, granted that using Aethersight apparently reduces the user's lifespan. (On the other hand, allowing the infiltration to go unchecked could result in far worse outcomes... it's not an easy moral question.)

Going back to the topic of 20/20 hindsight, while I admit that I'd forgotten Y'shtola could do this, as far as I know this is the first time she mentioned she could, so not even the other Scions knew it was an option for her to screen the troops, even if she was healthy enough to do so, and the talks could be delayed long enough for her to do so. They could not have been expected to ask her to exercise an ability they did not know she had.