Personally I am with Heartsbane on this one, and that it is entirely possible that Rheagar and Lyanna Eloped. I don't think any of Boaz's arguments against this happening would stand up to the idea that Rheagar and Lyanna were in love and people in love do crazy and sometimes stupid things without thinking of the repercussions.
One Big question that I have, and that may have come from over analyzing the story, is why the kingsguard felt they needed to die to protect Lyanna from her own brother. Did they think he was going to go in there and kill her or her baby? If she was in love with Rheager it can be presumed that they were there to protect her, not to imprison her. the alternative, that she was a prisoner, is almost not woth mentioning because it would have been far below the honour and skill of the kingsguard to act as gaolers or turnkeys.
The only thing that makes sense would be that they would rather die than bend the knee to the usurper being that the rebellion was basically successfull at this point. So that means that their whole last stand was nothing more than that, a way for them to die with honour, but that leads me to the enigma of BFS. How is it that after the Mad King died, Barristan was able to stop fighting for him and not loose face? Nobody ever regards BFS as anything short of honourable and nobody brings up the fact that he apparently turned cloaks. If a Kingsguard's oath dies with the king, why did the last kingsguard need to die at the ToJ? Barristan was always painted as bieng loyal to the Mad king (I believe there was a tale about him breaking him out of jail by himself, blindfolded and with one hand tied behind his back)