You can do a search in file explorer for all files containing the name fragment "EndActions" and delete them. There should be one per book, in the .sdr folder, and it is the file that contains the end-of-book data. If it is deleted, then it simply won't pop up, and that is ALL the file is used for.
Whenever you download new book, you will have to repeat this to get rid of newly downloaded book EndActions, but this should fix the problem generally.
If you jailbroke your kindle, there's ways to script this and turn it into a search command:
Kindle_Touch_Hacking#Search_Bar_Shortcuts