i've only seen your question noww, so sorry about this late answer, hope you are still interested in one:)
I have to say that it took me some time to come to like this ending, but I guess that what I found satifying about it, is that coming to like it felt like solving a puzzle, At first it was, why did they have to do it? there is no justification, and then it was well lets give it some thought, maybe since I found every thing else the writers did in this show smart, maybe there is a reason, and after giving it much thought, I can't say that I've solved the puzzle, but I can say that I found many beautiful ideas that I doubt that I would have found in an happy ending.
You said that the theme of this show was "sacrifice for the greater good" and you are right about that, but I think that the ending is kind of a criticism about that sacrifice. since just like Ddol Bok said in the early episodes, it's always the common people who pay the price" or who are making the sacrifice you've mentioned.
And that criticisn is kind of a statement against monarchy. I mean the king in this series is great, he is really thinking about his people through all of the series, and in a way watching this series could give you the feeling that Monarchy can be great under the right leader. I think that what the writers tried to say was that no matter how great the King is, In Monarchy it’s the little people that pay the price.
Even if the king’s cause is right, even when he is truly trying to better his people lives’, it’s still not a good way of governing, since the common people are the ones most likely to pay the price for the fights of the power going on. It may sound too simple but I think the writers aimed there since through all of the series it was Ddol- bok who questioned the big goals of the rulers and said that it were always the common people that paid the price, so when he said in this final episode “See, what did I tell you? The people have always bore their responsibilities through pain” shortly before he died, it just felt connected to that all of a sudden (I remember that when I first saw that episode, this line was kind of “why would he say that now” to me, but now I think that in away even though he believed in the cause and fought for it, he did it knowing the people would pay more)
I also think that this series was all about power to people, and the fight between those who believe that the people are capable enough to handle their power responsibly (the king’s side) and those who believe that people should be told what to do and be kept out of power because they are not smart or responsible enough to handle themselves (hidden root).
In a world where there is a king, and by his title he is supposed to decide what’s goods for others, So yi and Ddol bok can’t really live having any power, their happy ending at that time is just a fantasy of where the world should be headed, not where it is already. So I think that’s why they had to die, and why the show had to have the fantasy sequence of them in the end.
But Ddol-bok and So-yi weren't the only one died, many soldiers of both sides have died during this fight, and I think that that also had the purpose of showing the difference of dying for a cause, knowing what the cause is (the king's soldiers) and dying for a person, cause Karupae and Pyung had no idea what are they fighting for, and not really who is the person they are fighting for, nor do I think they fully understood what kind of person Garion is. all they knew was how to be loyal to him.
But most of all, even though there were many deaths in this episode and the lives of the main characters were not spared (sometimes I think it's just as wrong to save only the main couple and kill off the other who faught for them, especially if like the others more of course)
I found this ending hopefull, especially because of the scene with the king and the stubborn flower. For me it was a show about planting the roots (hangul) for a better future, and even though it took many years since that root gave fruits, it comes to say that by planting, your dying isn't the end of the story. planting root is what makes you win whether you die or live.
