Nokia designed Harmattan thinking that it will be the next major platform for them and they had to be serious about it. I think aegis-thing is mostly done to comply with common requirements from companies to have easily and securely wiped phones, and to protect users from malicious software.

You can see with mount command that they are using aegisfs filesystem for directories containing sensitive user data. I assume this is encrypted filesystem.
Can someone confirm that it has encryption? If it has, we probably don't need to take care of encrypting stuff by ourselves.

EDIT: It is possible that aegisfs gets enabled only when you start using MfE account, depending on Exchange server policies. It'd be nice to know more about when and generally what data gets encrypted.