First of all, I don't think heroes do more dmg or anything like that. They just effect ppl around them. Maybe faster capping, or whatever. We don't really know what the skills are that the hero posses.
But in terms of making sure that the server isn't fully packed with all heroes, I think the best thing would be to have maybe 2 per side max. And the way they are selected is you click on the class you want, then you check a box saying 'Spawn as hero'. Now you get in a queu. The next time a hero dies, the next person spawns as one. And this will go on till the reinforcements are to 0%.
Because ppl seem to think that the hero is a seperate class, but I think it's rather a 'hero version' of a regular class. So heroes can be snipers, assault, squadleader etc.