So, Bran told Jon about his true parentage because, as the Three-Eyed Raven, he knew the fallout that it would cause (Dany going "mad") and how it'd lead him to becoming King???
I'm pretty sure that this is exactly what's supposed to go down, and that Bran/Bloodraven is actively 6D chessing himself onto the Throne. It makes him who Danyeres pretends to be (sacrificing King's Landing for the good of the future by establishing the Republic-style Monarchy) and a much more grey figure.