I don't see this as "throwing away" her character development, but presenting her with a new challenge for her character. How she proceeds when presented with context, history, and the truth. Will she be like most of these comments and simply follow her base "need " for revenge or understand what precipitated the revenge and make a more nuanced decision?
Regardless of whether "justified" or not Soo Won killed Yona's father and potentially her. At the time she should be upset at Soo Won. However, it would be absurd to consider Yona flaky or indecisive when confronted with new information.
What I'm worried about is either King Il was manipulated into killing his brother. Or was a watching from the sidelines and allow him to be killed. Either act make sense for Soo Won's revenge.
What I'm failing to understand is how can people, who want Youa to take revenge for her murdered father, can't sympathize that Soo Won would want the same. Given how manipulative the church has been it's no surprise he'd want Youa dead too(which is taking it too far in my eyes). I don't personally believe in "an eye for an eye" but, I do sympathize for those who do.
I'm more upset that they've turned the church into a scapegoat/boogyman to blame for the discord between the brothers and by extension the cause for all the bad choices. It was much more compelling when the story was about the tension/mystery regarding these brothers. Now the solution to the mystery is religious zealots were the bad guy all along.