Its all a question of balance. If every member of your team picks a demigod with a stun ability (and I'd hope that not all demi's get one), then sure, you should be able to stun lock any opposing enemy demi god to get the easy kill. This is an easy kill and some teams may be inclined to min/max to get this type of combo. However, they are giving up that skill slot for stunning that could be used for something else. Perhaps an AOE nuke, a buffing aura, etc etc. The way the team uses their skills together is not only synergy, but teamwork. Good teamwork will always win regardless of the balance.
The thing to be on the lookout for are unbeatable combinations. Or in other words, if team 1 with demigods a,b,c, & d play together they are unbeatable regardless of the opposing teams skill/teamwork. It will take sometime before this becomes an issue simply because player skill (or lack thereof) will be the overriding element.