Your talking about the Allagans like they were a single entity. Do remember that the Allag population rebelled against their leaders.

The Allagans went really dark towards the end but that doesn't mean all Allagans were bad people.

Perhaps toward the end the crew of the Bismarck, unable to stomach the treatment of the proto Vanu Vanu, decided to rebel and smuggle the Vanu Vanu away from their incarceration. Perhaps the civil war was already starting and they decided to gather the innocent Vanu Vanu and escape the fighting. There are a lot of possibilities. Xande triggered the calamity because he was on the cusp of losing his throne and was trying to fast track his plan.