Like a few people have mentioned, I don't believe Bahamut wants or intends to destroy Eorzea. He was imprisoned for an extreme length of time, and pissed off to the fullest degree possible so he lashed out and took out his aggression.

We still don't know why the Allagans imprisoned Bahamut in the first place. I've been pondering if it had been out of fear. The Allagan's were an extremely advanced race so my thought is it had to be out of fear. Fear that Bahamut would be the only being possible to usher in a new umbral era. So they cast him into space. If true, that obviously was false because they died out.

Bahamut isn't going to run around and destroy stuff for any reason, so in the five years leading up to A Realm Reborn he probably went back to his lair and is chilling out, drinking some cow blood, watching the olympic eorzean games on his 250" magic tv. He'll defend himself if people come along, but I don't think he was re-imprisoned.

Of course this is just how I see it. However it is entirely possible Bahamut is the evil ass primal and was a threat to the world so Allags had to banish him.