After the battle of carteneau Kann-e Senna spent a week healing both Eorzean and Garlean survivors and order all Garlean troops be treated well and allowed to return to Garlean held lands. What we do have on the Eorzean Alliance doesn't indicate that they are in the habit of slaughtering enemies that have surrendered.

As for Castrum Meridium, it wasn't the Eorzean Alliance that blew it up. That was the Garlean's own superweapon. Its also not the first time that losing control of unknown tech has caused a Garlean instillation to be destroyed, killing everyone inside. That's how Cid's dad died.