I'd like to ask about the meaning of the phrase "close the book on one's thumb."
"Did you tell?" Do-ane whispered, closing the book on her thumb.
My guess is that she was holding her thumb on a certain page in the book and she didn't remove it when she closed the book.
Your explanation seems right to me - she used her thumb so she wouldn't lose her place while she was speaking. It is not a fixed expression.