well as far my understanding it is not issue..
you can always control what middlegen creates using ANT.
Their are two ways of solving this..
1) using ant task
<tablea generate="true" name="LIBRARY" />
<jointable name="LIBRARY_BOOK" generate="false" />
<tableb generate="true" name="BOOK" />
2) or u can control by table ...
now middlegen should generate mapping files for only LIBRARY table.and you can always add more <table> tags for more tables.
I hope that helps