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>