Oh my God. This fiction about a world with fire-breathing dragons steals some suggestive medieval practices surrounding strategic royal alignments and other made up stuff, and the knee-jerk reaction is to condemn it for exploring themes that are unacceptable today.
Perhaps we should instead condemn the series based on the domestication of dragons for use in battle to crush and fry opposing armies.
The series is a fictional exploration of a fantasy world with characters that embody human weaknesses, superhuman abilities and an archaic existence. Although the storyline harkens back to our own medieval history when women had much less agency than is true today (for most), it does so to allow storylines consistent with an earlier age.
So, although much of your analysis of Rhaenyra's relationship with her Uncle is a correct description of the storyline thus far, trying to drag the fiction into the present into our real world is like saying our history should be sanitized of all the evil that ever occurred and pretend it didn't happen. Oh, wait... there is a lot of that going on these days.
As the philosopher George Santayana said, “Those who cannot remember the past are condemned to repeat it.”