Put a dot in front of the audiobook folder (e.g. ".MyAudioBooks").
Then the stock media player will not see the audiobooks.
EDIT: If you don't want change the folder name: Make a file named ".nomedia" and put it in the audiobook folder. Same effect
EDIT2: If you use a file manager (e.g. EStrongs File Explorer) for the implementation, make sure the media player has indexed the changes at or in the audiobook folder.
I use the free app SDRescan for that.
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