So long as PvP and PvE are both in the mind of the class developers there can be balance with different classes.
The problems that arise tend to be when the game decides to add PvP or PvE into itself in a level the classes werent designed for.
Classic example would be WoW of course, none of the classes were designed around small group combat so when Arenas came to be it imbalanced things in favor of certain compositions. Then it essentially became a patchwork job that led to even more imbalances as the classes were changed.
So in my opinion if the developers set down in stone where the game is going in regards to pvp and stay the course things will be fine.
Also I think if things are designed around say 1 v 1, 2 v 2 or 3 v 3 scale battles and all the classes are viable in those areas everything is will work out at the bigger scales or at least be easier to adjust with out domino effects.
I had to laugh at the red cross equalling an easy target, in WoW Warriors and Healers have been the most unbalanced. Healing tends to be greater then damage cost wise.