In the content.opf in a random epub3 file I opened, the spine tag shows as:
To modify this, simply add the page-progression-direction="rtl" to the spine tag so it shows as:
Code:
<spine toc="ncx" page-progression-direction="rtl">
IIRC, the page-progression-direction is only supported in epub3 and even there some renderers do not support it.