Solution to the thm/blm cnj/whm Lore problem
I think the problem a lot of people have with the skill sets and the jobs can be played out through lore in the story. You dont have to take away the elemental nukes from CNJ and just cause CNJ has them does not mean BLM can not have them. I think a nice solution would come in how you quest for said jobs.
A thm could pick up the quest at his guild, and that quest could be to travel to Gridania and learn the ways of the conurers to increase their power. Their thirst for knowledge and power could lead them to want to learn the destructive forces of elemental magic.
A darker route could be that these thms would have to travel around and kill one of each elemetal and steal their essence to infuse it with their powers, i think either would work great with a professional write behind it.
As for CNJ the whm pop up as sort of a cult within the conjurers. They are enamored with light and holy elements so they rid themselves of their elemental powers and focus on using their bond with nature to heal instead of destroy.
This could also play in to the blm story line where these thm could end up getting a hold of these cast off powers to strengthen their own destructive powers. Or hell the quest could show both groups working together. The conjurers need a vessel for their elemental powers to enter so they can rid themselves of the destructive force and the thms step up to take them. There are tons of possibilities so don't worry about them having to change any backstories cause i dont think it is necessary.