As for OP's last question : why the Allagans didn't kill Bahamut but sealing him? Simple, if u look many other games / movie lores, u'll see that either:
1. They regard death penalty is ethically wrong BIG TIME.
2. Sometimes, to inflict more punishment and torture, its much better to seal them ETERNALLY wandering the universe or space or dimension or plane or whatever
3. Or, the third option is, the Allagan with their superior technology which could have enslaved Primals, valued Bahamut as a living weapon asset, which they can seal comfortably if they're not at war.
4. Bahamut is tied very closely to the planet, a surge of aetherial freed from consumption or leech from the Primals, may have devastating effects on a planetary scale