This problem has been around for a long time. Militias have been nerfed quite a bit in the past few years to reduce this. They actually disappear over time faster now. It is a hard problem to solve. If you make militias too weak, large realms will just run over small realms. If you make them too strong, it becomes too difficult to siege cities. But then there are plans to make the whole thing more interesting. I'd wait for Anaris' new trading system. That will allow you to starve cities again meaning it doesn't matter how many militia units your enemies have as long as you can cut them off.
