In the manga, Kuu "dies" the same as in the anime, but Kyoushiro and Setsuna know that it will be hundreds of years before Kuu is reborn.
So the manga ending gets probably gets a little controversial here.
Many years later, Setsuna finds Kuu reborn (not as a child; she's grown to her "old" self) and reunites her with Kyoushiro, who has apparently been reborn in Kyoushiro and Setsuna's son or descendant.
They don't say how many years have passed. (although it's been a long time because the castle visible from the hill, shown in the manga ending, is mostly covered in foliage) Obviously, because they knew it would be so long before Kuu was reborn, Kyoshiro and Setsuna knew he would never be able to see her again in their lifetime, so this was the only way Kyoushiro coud ever see Kuu again.
The ending clearly shows that on their travels together Kyoushiro and Setsuna had a child, and the man who Setsuna brings to Kuu calls Setsuna "mother." Whether this man is Setsuna and Kyoushiro's immediate son or a later descendant born from Setsuna isn't confirmed.
And this would be the part some may find controversial; being a Setsuna fan I particularly like it, and even not as a Setsuna fan I like this ending, but some may question Kyoushiro being in love with Kuu while having a child with Setsuna. But it really was the only way for Kyoushiro to meet Kuu again; obviously this is some time after Kyoushiro died as he's nowhere to be seen, and both Setsuna and Kyoushiro knew that Kuu would likely never be reborn in his lifetime, thus why they did this. Although Setsuna makes it clear in her narration of the ending that she still loves Kyoushiro, she has accepted that he loves Kuu and has devoted herself to reuniting them, and this is the only way it would ever happen. But just to be clear, it's not like Kyoushiro is still using Setsuna; he treasures her probably just as much as Kuu, but they both know and accept where his love truly lies.
So like I said, as a Setsuna fan or not, I really liked this ending. And besides, some people found the anime ending jokingly controversial, since it was a middle-aged Kyoushiro being reunited with a child Kuu.