Yes, I agree with what everyone said. I think that Riza does carry a lot of guilt for what happened in Ishval and what the flame alchemy she gave Roy turned him into in 94 and 95, and I'm sure Roy feels guilty as well, so they're both trying to atone. Of course, I don't think that's the only reason they stick together
You're right, it's not the only reason why they're together. We seem to forget, sometimes, but Roy is the closest Riza has got to a family! The bound between them is way to deep to resume only to guilt, but they both blame on themselves for Ishbal. Roy thinks it's his fault Riza became a murderer and Riza thinks it's her fault Roy became a murderer. They were both yound, naive and idealistic and they payed a big price for that.
But, the thing about Riza's guilt is that, on that particular scene, you get to see how much she blames herself for everything that has happened. If Roy failed at that point, it would mean Riza failed, too. Almost as if she failed him, cause she promised she would try her best keeping him from falling. She's not his aidee to protect him from enemies, he can take care of himself in that dept. She's there to protect the 'Leader Roy' from his own ingenuity and his own darker side. He's just too powerful to go beserk....
And that only makes the 'queen' allusion even more impressive, since, in myths, that's exactly the figure and function of the Queen: to be the King's conscience and keep him from driving from his path. Whenever a king looses his queen, he begins to loose purpose and meaning and cannot rule anymore. And it's fantastic to see Arakawa put such a reference in her story.