I agree that setting a Mail Preference to leave messages on the server defeats a significant aspect of POP mail. Having said that, my iPhone is set to NEVER remove mail from the server. That's because I use a MacBook Pro laptop as my primary device, and on that device the preference is set to remove messages after they are retrieved. The only mail reaching my iPhone is mail that arrives when the mail client on my laptop is not logged in and that works fine for me because the iPhone is not the primary device I use to retrieve mail.
Until Apple releases a fix here are two suitable workarounds that do not involve having to leave mail on the POP server:
1. Remove the attached file from the email message and store it elsewhere on the phone. Eg. once a photo is saved to the Camera Roll it resides there and will not be compromised even if the email in the Inbox goes dark. That's the simple route, but even better...
2. Backup the phone every day to a source that is not using iOS such as an iMac, MacBook Air or MacBook Pro. That rules out backing up to an iPad. Once data is saved to another device it cannot be impacted by the mail app on the iPhone. IMPORTANT NOTE: - you can rely on an iCloud backup BUT ONLY if you first move the files out of Mail as referred in (1) above because an iCloud backup will not save email messages. It backs up the mail app and settings but none of the messages.
The lack immediate response should not be misinterpreted as lack of concern by Apple. During 30 years using Apple products I've experienced an incontrovertible commitment to client service and satisfaction. That coupled with superior products is why I use Apple exclusively in my business as well as for personal use.
Please keep using the feedback link and urge others to do so. It will only accelerate the process.
http://www.apple.com/feedback/iphone.html