Here is my concern about removing carriers:
Originally Terran had their Thor's altered/removed for the implementation of warhounds, which made the concept of removing another classes units seem a tad bit more fair/balanced. But now Terran and Zerg keep EVERY unit that was in wings of liberty. i no longer see a logical reason to remove the carrier.
Is the concept of having carriers with the tempest (the new capital ship) OP? Well it might be except for the fact that it would take ridiculously long in the game to pull it off. This combo wouldn't be something someone can rush and get away with. Lets not forget that both units need their individual fleet beacon upgrades to be worth while. I think it would be unrealistic to assume that this combo would arise in most pro/ladder games. If by chance it does and is still OP, just change the purpose of the tempest in the Protoss ball.