The problem with that is Daenerys herself. She felt like she was supposed to be the devine ruler by her lonesome and she felt like since she was a woman, her ‘right’ to the throne would always be contested by some who felt like a man (especially a man in her family) should rule
If Jon was the rightful heir and Daenerys wanted the throne, why wasn’t the obvious solution for them to just marry and rule together?
Jon had the claim. Dany had the army, dragons and experience.
And them being related shouldn’t exactly have been the dealbreaker, they’re Targaryens. That family tree has seen worse.
Instead, the story chose: “one of them has to die.”
So was the real problem that they were related or that Dany couldn’t accept Jon had a better claim?