Kollel_Wife,
I definitely understand your concerns. Firstly, are there any jewish libraries in your area? There are many mystery books available from jewish publishers.
Secondly, if you do plan on going to a regular library to look for “clean” books, most libraries have a juvenile section, where many of the books are clean. Of course some aren’t, but it shouldn’t be that difficult for you to figure out which ones are clean and which aren’t. Or, if you want to limit the types of books (such as not taking out fantasy books), you should be able to easily see what type of book it is. Also, there are many classic authors, and you can ask a librarian who they are, which do not have this type of issue.
If you do happen to a regular library together with your child, you should be able to tell them in advance that some books in the library are not good for their Neshoma, and that they can only take out books after they show them to you.