I was thinking something along those lines, like a "corruption" (for Mordor, say) or "purification" (for Imladris) meter that allowed you to recruit increasing numbers of troops as the conquered area was gradually turned more towards your faction. It's just a brainstorm idea, the actual mechanics and coding would have to be worked out.
Maybe you could even take up quests from town elder types who are trying to convert the land to your people's way of life. For example, resettling refugees from Dol Amoth to a province in Harad to "Gondorize" it slowly.