Fortunately for Karyn, she had not made a direct wish "I wish Jon would turn into a tree". Therefore becoming a tree actually was reversible.
Even more fortunately, she had wished Jon could decide what she would emerge as.
To decide what she would emerge as he had to be able to decide--which meant he could think, after all, even though most trees never do that.
By the time morning came, Karyn had been completely absorbed into the tree, and Jon suddenly awoke. He realized that Karyn was a vague mass of chemicals inside his system and that he could decide what she would emerge as.
