Targaryens are above the laws of men. That's why they could marry their siblings, and they also practiced polygamy as well. Who's to say that Rhaegar, a known traditionalist, didn't decide to revive the practice and marry Lyanna in the South? He would be a true born son of Rhaegar and have a better claim than Dany, although if he was smart he would marry her for the sake of the realm and allow her to rule, he taking at most a joint power position. Jon values the good of the realm more than his own ambition and I think he would want to secure Danys help against the Others at any cost.

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