Well, there could be a script when she dies that makes all the right people know she's dead so that you don't go around looking for her. And of course you get to complete the main quest. Just make a new character.
"But I don't want to start all over! :angry: "
You don't have to! Keep the character who can't complete the main quest, because that character's story can still move forward. And make the new character have completely different skills. If it's a good RPG, unlike Oblivion, different skills will make the experience totally different the second time around, so you're not starting over.
And while your original character focuses on factions (because there are TONS of factions to keep you busy for hours), your new character can do the MQ. What are the odds that the queen will die two times in a row in that same way? Pretty low if they tested the game properly.
And, yes, by the way I would be like, "coooool." I love when my characters fail epicly and unexpectedly. I feel that RPG's are about making a story. You're not trying to beat anything. A broken main quest isn't "game over" if it's a good RPG, a broken main quest just steers the story in a new direction.
Because there's SO MUCH else to do besides the main quest. Let me emphasize that again.
The main quest being ruined through no fault of the player is ridiculous. No, an Elder Scrolls game is not to be completed, but who wouldn't be angry about being five hours into the game and being told "So and so are dead. You have failed to fulfill the prophecy." when they didn't do anything to harm that person? Also, for those other quests:
1. The travelling merchant who was robbed and needed your help was killed by monsters on the road.
2. The quest giver with a lower responsibility stole an apple and was mercilessly beaten to death by guards.
3. You steal an apple and as a guard comes to arrest you, you resist arrest. The leader of the Fighters' Guild has a high disposition towards you, comes to your aid, and gets slaughtered. The guards accidentally hit quest givers and all people with a high disposition towards you come to your aid. Several quest givers die in the process, just for simply stealing an apple(why have stealing in a game if its consequences are that major?).
4. Mythic Dawn agents come after you and quest givers, who help you, get slaughtered.
5. The emperor gets killed by a rat before a Mythic Dawn member can assassinate him.
Things can and do go go wrong with an actual AI system(which Morrowind lacked). That's why Bethesda had to dumb down their original system. Perhaps the essentials are even a leftover from that. I was walking near Chorrol recently and noticed the dead body of a local skill trainer who hunts everyday. A bandit killed him. There was nothing I could do, because he was already dead. In Fallout 3, caravans aren't essential, and while roaming, they(easily the best merchants in the game) may die when you can't do anything to save them. For this reason, I try to avoid exploring areas along their routes, which isn't fun. There are travellers in Oblivion(actual travellers) and their deaths, which have nothing to do with my actions, can be a pain.