This is different from commanding your troops like an RTS. The creeps are still, for the most part, uncontrollable critters that run around and fight for you. They still act as an endless stalemate that waits to be broken by the Demigods. This isn't a full RTS style control scheme, but some amount of control would be most welcome. I like the idea of preset waypoints that you can change between.
I don't like the idea of them being tied to a Citadel upgrade. I think you should be able to change them anywhere from the beggining. I think it would throw a chaotic, fun, and most importantly tactical spin on the current early game.
I disagree that only generals should be able to do this. Having a General would become a necessity. Random community games would be disasterous if one team was only Assassins, and 1v1 Assassin vs. General would be decidedly in favor of the General. Or Generals would have to be very weak to compensate, and thus all competitive 5v5 teams would be 4 Assassins and 1 General.
Instead of just generals, I think that one person would have to be the "creep manager" for each flag. Here's what I propose. In the lobby, you put an option that basically says if you want to be a creep manager or not. If you check it, then you are telling the game that you want to command the creeps. The starting portals are then randomly divvied up between the creep managers. If there are no creep managers, then the starting portals are just randomly divvied up. If you capture a portal flag, then you become the creep manager for that flag. It would also be critical that you would be able to give your creep manager title for a specific flag to another player.