I can imagine nothing pissing off a noob more than getting a virus within 10 minutes of play and having no idea how to stop his ship from self destructing.
Perhaps this will need some sort of firewall system built in where ships cannot communicate unless ports have been explicitly opened. Perhaps some sort of communications proxy that can serve for safe communications.
It could have a system similar to EVE where high security systems have infrastructural to mitigate risk whereas low sec systems lack this but contain the best rewards.