I think it's obvious that Gypsy knew she wasn't actually sick. If she could walk, but had to be in wheelchair, obviously she knew. If she wasn't retarded, but had to pretend, then obviously she knew.
If she didn't need the huge glasses, but had to wear them, then obviously she knew.
If her hear wasn't falling out, but was shaved to fool people into thinking Gypsy had leukemia, then obviously Gypsy knew.
But this kind of deception was going on for years. Clearly it wasn't Gypsy's idea to pretend to be all these things. Based on what I know, I don't doubt Gypsy hated her mother and wanted to get away from her.
When she previously run away, mother found her and brought her back. When police previously came to check on Gypsy, nothing was done.
So, Gypsy could have thought that the only way to get away was to get rid of her mother.