I remember reading a book early 2000s, it was a fantasy novel from my high schools library. It was about a girl transforming into crystal that caused her excruciating pain. She was traveling to a crystal castle/pyramid/palace on a boat and during the trip one of her companions could help her by taking her pain and experiencing it himself for short periods. I believe that at the end she integrated into the castle itself. I also have Neil Gaiman in mind when I remember it but I don’t see it in his book list.
This sounds reminiscent of Echoes of the Great Song by David Gemmell.
One of the main protagonists is a girl transforming into a crystal being after becoming 'crystal-joined' when a crystal is used to heal her.
They are fighting an invading army from an alternate timeline where she(or another woman, I'm a little hazy on this) had already transformed and was encased in a pyramid like structure where people were sacrificed to extend her life.