I also dont agree that it will be a balancing nightmare. It'll take a little more effort, but its doable. We already see professions with distinct roles (Guardians on point, Warrior/Engineer as Roamer, Elementalist as Support etc). No one is equal anyway at this point. And this will persist into, for example, a CTF.
Guardian protects your base flag, Necro/Ele breaks open the flag, Engineer/Warrior grabs it and runs it.
The same strong points that get them certain roles in Conquest will get the similar roles in CTF, because there is a need for similar roles.