Well when a General can kick an Assassins butt without even relying on their army of units for assistance there are definately balance issues. Why play an inferior hero?
This is a misconception really. Generals were originally supposed to need their minions to get things done, but then the developers decided this would be too difficult to accomplish and now the Generals can essentially be played like Assassins if the player so desires. The minions hardly even make that big of a difference, anyway. The pure Assassins are still more powerful in terms of damage.
If you think there are balance issues now, you should have seen the game before the day 0 patch. I haven't seen anything approaching a balance abuse yet.