Kyran decided not to remove the Tower of the Ancients from the space it fell to. But that did not mean he would pass on the opportunity to use its benefits.
As Cyneah had pointed out, letting his people enter and challenge the Tower of the Ancients would improve their knowledge and magic level. Kryan's only concern was their survival.
The difficulty level of the Tower of the Ancients was higher compared to the Tower of Tribulations. Kairos already confirmed the latter was made to cater to mages in the Lower Realm.
Considering this point, Kyran wanted to study how the tower's system worked with the assistance of every Ancient hiding inside. He would then find a way to ensure his people's safety as they navigate through the tower.
Since the Ancients were needed for Kyran to accomplish this, he had to keep them alive.