In Battlestar Galactica, the Colonial fleet is separated from Galactica when they are forced to jump to the emergency FTL jump coordinates. Battlestar Galactica is left behind, and after they realize that they must go back to Kobol to calculate the jumps, they decide to network the computers to make the calculations take less time.
This involves connecting the computers responsible for communication, navigation, and the engines. Linking the computers does not involve networking the computers with any external ship or server, as there are other friendly ships in the location.
So, how does a virus, only present in another data system completely separate from Galactica's, manage to introduce itself into an environment that it has no contact with?
If Galactica has no outgoing communication, there is nothing for the Cylons to 'hack' their way into.