I'm of the mindset that says that afflictions are a form of psychological warfare. Not all afflictions are damaging in combat, and even those that are aren't always crippling. The AI likes to invade me with armies of Niefel Huskarls that it can't feed, and they all wind up diseased, but it doesn't make them noticeably worse at taking down undersized armies. But I know I hate to see that ugly red heart on my commanders (even if it's something harmless like battle fright), and I don't like it on my shiny new armies either.
Anyone who plays Pangaea is probably immune to this feeling.
-Max