Well if it's any consolation if you're stuck on they all die
In the good ending, we know for a fact Chaco and Santa survive... since it shows them in the copter in the ending, and in the transformation scene.
Soon there will be Mimigas of all colors!
And I'm curious... You do know there's a Best ending besides the just Good ending don't you?
EDIT: Also, you notice that all the Mimigas are gone when you go to fight the Doctor right? Just a few standing guard before the Throne Room... That means they already have begun their attack on the surface. Meaning most of them were probably already on the ground.
After the Core is destroyed they should have turned back to normal if Kazuma is right. So most of them should survive...
EDITEDIT: Plus, the ending does show pictures of Jenka still in the Sand Zone, and Balrog helping out at the Clinic... The Island may have fallen, but it should be fine, probably due to magic! I mean the falling scene didn't show the island falling apart, and it sure seemed to fall slowly...
EDIT: Well at the very least we know that some of its inhabitants survive... by the ending, if the island is destroyed...
Hmm... let me think of the implications of how the island falling would be bad...
*SPOILER* highlight to reveal
If the island falls, perhaps Ballos is released from his imprisonment; or perhaps the effects Ballos has will begin to spread across the land, like a bad seed. Over time it could really become a serious problem even if Ballos is still imprisoned..!
Also, yes; I sure would imagine that the island should be majorly damaged. From the tragic looking end scenes showing the pictures of the places you visit as it shakes to pieces...