You need to open the ePub in an archive program (they are just ZIP files) and add an XML file to the META-INF folder.  This file should be named com.apple.ibooks.display-options.xml and should have the following content:

<?xml version="1.0" encoding="UTF-8"?>

<display_options>

<platform name="*">

<option name="specified-fonts">true</option>

</platform>

</display_options>