The role-playing parts are for the player. They have nothing to do with the Warrior of Light. The Warrior of Light is not in any way affecting them. You're not "controlling Y'shtola" as a Warrior of Light. You are simply shown the battle she had from her perspective as the player.

This is both so that you know the FULL story (Alphinaud's case) and...just for a change of pace (Y'shtola). It's absurdly common in all fiction. It's the least common in games, but even then there are cases where it's present.

And it's not like they are "jobs". Seriously, two or three abilities that are seriously overpowered is not something you can reasonably fail with nor something you'd need to study to use. Don't like it?! Well, no one forces you to like it. However removing them would mess with far more people than keeping them, while delegating them to optional content would be equal to you skipping chapters in a book then asking people what happened when you'd come across unknown reference.

In other words...sorry, but you'll have to "deal with it" somehow.