I’m an FtP player and is mostly coordinating the war for my guild. Sure i’m not in one of the top guilds. But the off duty heroes are applied to both teams during the attack phase. So it is still rather fair. There are more to this game than merely building one strong team (in this case 3).
If your best hero gets put out of duty, consider a different tactic. Instead of having a strong-medium-weak lineup, go for a balanced medium lineup and attack an opponent of similar build. There are 9 cars to choose from.
Considering the number of players are involved in 1 war, i would say the chances that the off duty heroes are the ones every single player in your guild uses are rather low. And if not for the off-duty heroes, war will simply be another coliseum.