Manning had Top Secret clearance, even if his leaks had no top secret documents in them. But hey, lets throw the book at him anyway.
Microsoft Windows started offering built-in encryption in Windows 2000 Professional (Encrypting File System) and full disk encryption (bitlocker) since Windows Vista Ultimate. Using encryption isn't some arcane feature only used by UNIX gurus.
The NSA puts its stamp of approval on certain encryption cyphers (i.e. AES) and actively helps strengthen some of them (DES).
Their own policiesdictate that top secret documents must use AES 192 or 256 bit encryption. I suppose that might only apply when transmitting documents out of their network or whatever, I dunno.
Encryption can be used to prevent system administrators from viewing the data they administrate; some cloud providers offer client side encryption/decryption. Mega upload's new service is doing that, for example. Perhaps the NSA could outsource to Kim Dotcom.