There is something fishy going on when deploying email profiles to iOS devices using Windows Intune and ConfigMgr 2012 R2. When you have deployed an email profile to an iOS (7.1) device you cannot choose to send pictures from that email account, as the account is then missing from the drop down menu when choosing “From”.
If you go into the Mail app in iOS and then write a new mail then you can choose the deployed email account, the problem is just related to sharing pictures (possibly also other stuff) via the “Share button” > Mail feature in iOS.
Note: If you go to Settings > Mail, Contacts, Calendars you cannot see the email account listed in “Default account”.
UPDATE: Turns out that this is indeed not a bug but a feature. You must activate “Allow email to be sent from third-party applications” in the email policy.