"Not your typical windows desktop"
Maybe not, but laptop based scanning & sniffing tools will soon expose open ports and capture and analyze traffic going in & out of the server including interfacing app ID's and passwords (even if encrypted). Non-mainstream O/S's did not stop Flame or Stuxnet which were specially crafted to target SCADA systems. It is not beyond the bounds of probability that sooner or later the bad actors will figure out how to craft malware that has been specifically tailored to interface with aircraft borne servers such as the T7.
The prospect of Windows like O/S's being used on the 787 and A340's is even more scary.