Hi Tom.
You are correct, the Cures Act is focused on the more electronic aspect of medical records. It also, however, focuses on patient choice. If the patient does not want to use the portal and prefers that you give them the medical records on paper, then that is perfectly fine. Its will be up to the patient how they receive their records.
As far as patient's interpreting the notes, I have not seen that as part of the Cures Act. It is definitely a possibility that patients will read the notes and interpret things the wrong way (Thanks, WebMD). I think this is something that may just be handled at the office level. Its no different than if patients received a copy of their medical record on paper and read them. Its just the delivery method has changed. As far as a secure email/messaging system. You already have that with the patient portal.
