What has been done to provide security for remote wireless updating of in-aircraft software components?
Boeing claims in this document:


  The 787 uses wireless (802.11 b/g) technology while at the gate to
  transfer maintenance data and update the Electronic Flight Bag (EFB).
  This is referred to as “e- Enabling” and it will allow airlines flying
  the 787 to operate more efficiently.


So, yes, they use a regular WLAN connection for transmitting data while on the ground.

The document continues:


  Upon weight on wheels the 787 attempts to authenticate specific ground
  access points. Information regarding the key configuration
  requirements and how the 787 authentication occurs requires the
  signing of a PIA.


I interpret PIA as Proprietary Information Agreement, a form of secrecy agreement. Boeing uses security through obscurity to safeguard the integrity of the connection.

If you want to know more, Boeing advises to contact 787terminalwireless@boeing.com. However, I doubt they will talk to you or me unless we are airport representatives with a credible need to know.