It's an iBooks question
That means all your other users (including iPad owners) will have to live with that.
There is an editor who produces EPUB in two versions, one with embedded font and the other without, because of this kind of limitation. Maybe you could do the same?
http://efele.net/ebooks/
If you use W2X, it's just an option to tick when exporting to EPUB (
image with relative size or no)