In regards to Rhaegar and Jaehaerys II, your argument is essentially that the ends do not justify the means, which is why you bring up Ned fighting for Daenaerys' life. How do you then explain GRRM's hard-on for Bloodraven? His entire history is the "ends justify the means," which is why he murdered his nephew in cold blood and instead of truly being punished, he gains superpowers and then gets to become king via Bran (as it has been confirmed that Bran becoming king was GRRM's idea).
We clearly have very different opinions on Bloodraven’s story because I certainly don’t view it as any kind of validation or personal victory. Brynden Rivers went from Hand of the King and the de factor ruler during the reign of Aerys I to being sentenced to the Wall for a crime, losing his position, power, freedom and the woman he loved in one go. He was punished for what he has done, whether that’s being sent to the Wall for murdering Aenys Blackfyre or being hated for abandoning vassals to fend for themselves because he was too focused on Bittersteel and the Blackfyres.
Moreover, painting Brynden’s magical powers as some sort of a prize he gained for his actions is a misconstruction. First of all, magical powers aren’t inherently rewarding as poor Daeron the Drunken would tell you. They can be a burden and a curse. I know that some in fandom treat magic as an award to be given to the most worthy and a mark of distinction to denote a character’s specialness, but magic is not tied to morality or integrity in ASOIAF. Indeed this is a story where Euron Greyjoy is one of the flashiest magic users in the story and he is an absolute horror. Magic is generally not treated as a reward within the story but more of a struggle. Look at Bran Stark. Look at the Ghost of Hight Heart. Look at Daeron the Drunken and Daemon the Dreamer. How much did any of them enjoy their magical powers? How much is Brynden enjoying his? The guy has turned into a tree.
The sight of him still frightened Bran—the weirwood roots snaking in and out of his withered flesh, the mushrooms sprouting from his cheeks, the white wooden worm that grew from the socket where one eye had been. He liked it better when the torches were put out. In the dark he could pretend that it was the three-eyed crow who whispered to him and not some grisly talking corpse.
One day I will be like him. The thought filled Bran with dread. Bad enough that he was broken, with his useless legs. Was he doomed to lose the rest too, to spend all of his years with a weirwood growing in him and through him? Lord Brynden drew his life from the tree, Leaf told them. He did not eat, he did not drink. He slept, he dreamed, he watched.
This is the Brynden we meet in ADWD, the one with the superpowers.This is not a triumph, it’s a horrifying fate. Brynden is no longer a person but a magical vessel. His memory, his personality, everything that makes him Brynden Rivers has faded, substituted by his function as a greenseer and a mentor waiting so long for the last greenseer, withering and fading and growing weaker as the years flew by - a mentor that will die, that has to die for Bran to come fully into his own. Bloodraven isn’t becoming a king via Bran because very little of the real Bloodraven’s consciousness still exists and even that part will eventually go into the weirwood network to join the rest of the singers as Bran takes his mantle.
So yes, Brynden did operate on the notion that the ends justify the means but where did it get him? As Hand, he was so focused on the Bittersteel and Blackfyres that he had the crown abandon its feudal obligations towards its vassals which not only played a role in stoking the dissatisfaction with the Targaryen dynasty but weakened the legitimacy of the same monarchy he was trying to defend. As a greenseer, he may have empowered a madman like Euron in hopes that he’d be able to help in the fight against the Others, except Euron is working against humanity and will probably be the one to unleash the Others on the realm. So the story isn’t validating Brynden’s philosophy, it’s showing a pattern where his ends are constantly jeopardized by his unworthy means.