For the system to work, there should be a dynamically running ecosystem, but one that could be... let's say, nudged. The system would need to be constantly monitored, and advantages could be silently inserted on a losing side to bring things back on track. Of course the entire system would need to be designed with this in mind. Having buffer pools that actually work even in the presence of players would be another key thing though I think.
Yeah a zerg... that could happen if you did that. One counter to that could be to force the spawns to not group up by involving some sort of AoE or something... That will cause an "AoE analogue" to the zerg though. Another idea could be resource management. Either in the form that troops that need supply, supply trains or whatever takes a certain amount of space, or there is a maximum supply flow on a certain route, making a zerg starve itself down to size. Or resource nodes of some sort that needs to be defended in order to support the army, so that you force the spawns to spread out.
Or, absolutely, accepting that the system falls. That doesn't fit so well in MMOs though!