Unfortunately, I think a large segment of this theory rests on a mistake by GRRM. The quote that Preston uses, about Eddard not thinking of Rhaegar for years (Eddard IX), seemingly is impossible. It comes after several conversations that Eddard has about Rhaegar, in at least one of which (Eddard II) he thinks about Rhaegar. I'll just highlight the pertinent parts from the conversation:
"Your Grace, the girl is scarecely more than a child. You are no Tywin Lannister, to slaughter innocents." It was said that Rhaegar's little girl had cried as they dragged her from beneath her bed to face the swords.
"Nonetheless," Ned said, "the murder of children... it would be vile... unspeakable..."
"Unspeakable? the king roared. "What Aerys did to your bother Brandon was unspeakable. The way your lord father died, that was unspeakable. And Rhaegar.. how many times do you think he raped your sister? How many hundreds of times?"
The time had come for Robert to hear the whole truth, he decided then and there. "Do you remember the Trident, Your Grace?"
"I won my crown there. How should I forget it?"
"You took a wound from Rhaegar," Ned reminded him.
There's also a bit of a change when it comes to Ned's promises. Unlike in the video, at one point Ned thinks about the harsh consequences of the promises he's kept. It's only after he's been attacked and imprisoned that he thinks of the promise being broken. That's a fairly massive shift for Ned, to the point where he's started to resign himself to death. If he's dead, he can no longer protect Jon and he'll never be able to tell him who his mother really was. That seems like the more obvious explanation to me.
On the other hand, he does highlight an interesting juxtaposition I'd never noticed before. The memories of the promise do seem to be exacerbated by discussing Dany.
Edited by Doorlocks, 18 August 2014 - 09:27 PM.