So Why assume removal of Classes?

[Exodus-E]

Thief-Rolled into Ninja/Rogue

By that logic, Ranger was rolled into Archer/Bard...but it could still exist as a proper job later on.

Geomancer-Rolled into White Mage

Nope. Geomancer skills were dependent on the field they fought on, and while Conjurers/White Mages DO use elemental skills, it's not the same.

Chemist-Have it

Nope. Alchemist (DoH) is NOT a Chemist.
Chemist was a job that mixed up items in actual combat.
But given Yoshi-P's stand on combat-based classes not using consumables for their skills, then it's unlikely it'll happen...unless it's altered in some way.

Puppetmaster-No comment (Isn't this similar to Beast/Summoner)

In that it's a pet-based job? Sure...but the similarities kind of end there.
What made Puppetmaster different, is that they could "customize" their puppets with different parts to change their purpose and stats.