Defeating the Aeons to make Yu Yevon run out of ways to hide sounds reasonable, but I still think it was a bad plan. Yu Yevon needs an Aeon to create Sin, right? After you defeat Jecht, Sin is dead. Yuna and the others could have just left Sin after that. Yu Yevon would have been without an Aeon to use, so Sin would have been gone for quite some time. Of course, that would mean Yu Yevon could come after other Aeons some day, to create a new Sin, but seeing what kind of a coward he is, with his style to run and hide behind unholy Aeon-armor, I don't think he'd dare to come out and try to obtain a new Aeon. So he'd just mourn his loss and weep for the rest of his days and never become a threat for anyone. Sure, he would be still alive, but he'd be as good as a general without an army or any resources, i.e. powerless.