Great example. In this case it certainly served a story purpose to actually show the act, Drogo continuing the domination of a submissive Daenerys...the baseline of her character arc and transformation to a powerful leader.
Not to be a prude, but I actually hated this scene and found it offensive. Oh, so she can only transform as a woman through sex? That's what that scene had me thinking, that she wouldn't have otherwise been a great and powerful leader if Drogo hadn't asserted sexual dominance over her.
I think both of you maybe missed the point of those scenes. It's not about Dani submitting to an abusive Drogo. It's about her accepting even this aspect of her role as queen.
Yes, that acceptance is a tremendously important part of her development as a character. It's also an important distinction to make because it's what helps her to rise above her helplessness and the perception that she is a victim.
She is Queen, and she is willing to take ownership of everything that means.