If I'm not mistaken, Saadia tells you that she spoke out against the Thalmor and now there's a price on her head. Well, Hammerfell just so happens to hate the Thalmor with a fiery passion. I turned her in upon hearing her story, because she took me for a fool.
Well, she lied to you. That's not lore-unfriendly, that's just a lie within a game. Different characters, different agendas, it's what keeps Skyrim interesting.
Dagmar, thanks for the huge write up, I'll try and respond.
1. Appearances can be deceiving, especially if they are in graphics. I think Bethesda just didn't make her look old enough.
2. This was most likely her lie.
3. If she implied that Hammerfell was Thalmor-controled then she was lying again. You've gotta think that the average Skyrim citizen doesn't know too much about the world.
4. Saadia's lying again.
I'm not saying that this quest was well written, it wasn't, it was confusing at best. However, I think that all of these contradictions you're finding are lying on the behalf of the characters and not inaccuracies on Bethesda's part. Bethesda is generally very good at being lore consistent, but poor at in game story telling, I just think that this quest is a microcosm of that.
That all being said this quest wouldn't be a great starting point for another DLC.