This is more a problem you've created based on your assumption of how the system works, rather than a genuine issue.
The system could simply work that each class has say, 2 specialisations that are totally seperate from the rest. Marauder could specialise as Dark Knight and Warrior, for example. Thaumaturge and Conjurer could specialise into totally seperate jobs.
I dont really understand the logic behind them developing a '5 job rule' to each class, because 5 jobs per class is completely unrealistic. It would be easy enough to create two for each (A gladiator could become a Paladin or Berserker for example, dual-wielding swords).
Also, gladiator has absolutely nothing to do with thief or red mage in terms of skills. It seems you're creating a really vague and unconvincing arguement for why it wouldn't work when your approach is totally convoluted to begin with.
I think it's basically a given they're going to be linked to classes, and it's fairly easy to do so.