I would save images at the highest resolution you think your content will be viewed at. In your case, retina resolution. You can always scale down to a lower resolution, but you can never get back what isn't there. Even better, read this:
and use media queries to deliver different content to different devices. iBooks and most other modern eBook readers should handle media queries. Be sure to put the media queries in a separate
CSS file, because Adobe Digital Editions ignores the entire file if they are present. Use this to your advantage.
BTW, if you're seeing obvious scaling artifacts, that might indicate that you aren't dealing with true photographic content, and you should consider a vector-based format like SVG instead.