I’m looking for a film (possibly a made for tv film) about a kid undergoing treatment for some disease. They are also writing a fantasy story while dying. I think the doctor treating them was in the fantasy story as an evil witch. The movie was from the late 90’s early 2000’s (at least that’s when I saw it)
The question rang some faint bells in my memory. Funny thing is, after looking around a bit, I am pretty sure I was not recalling the same story.
However, a New York Times article/review from 1995 seems to fit all the details in the question. You can see the article at http://www.nytimes.com/1995/08/11/arts/tv-weekend-boy-s-short-life-blends-with-a-fantasy-he-wrote.html.
The boy who wrote the story was, according to the Times review, named Christopher Millard. His story was called "The Four Diamonds" and it was based in Arthurian legend. The TV movie included a character played by Christine Lahti (didn't she play a doctor in "The Sopranos" as well?), a witch named Raptenhad.
It sounds a bit like Paperhouse which was released in 1988, but has been shown on TV a number of times over the years (which is where I've seen it).
In the story, a young girl is in hospital with glandular fever, and meets another patient. She ends up entering a dream fantasy based on her experience in the hospital and on her drawings, including an angry man created by her accidentally drawing an angry face on a representation of her father.
I can't quite reconcile the doctor being a witch in the dream fantasy, though.