Hi,
I have a solution.
Download Karabiner.
Google "karabiner app specific"
Then copy and paste this to your private.xml file:
<appdef>
<appname>IBOOKS</appname>
<equal>com.apple.iBooksX</equal>
</appdef>
<item>
<name>Change ScrollWheel</name>
<item>
<name>Change scroll for page_down_up</name>
<identifier>remap.scroll_page_down_up</identifier>
<only>IBOOKS</only>
<autogen>
__ScrollWheelToKey__
ScrollWheel::UP,
KeyCode::PAGEDOWN
</autogen>
<autogen>
__ScrollWheelToKey__
ScrollWheel::DOWN,
KeyCode::PAGEUP
</autogen>
</item>
</item>
Cheers,
Ttan