definitely. although, with all the talk about cylons being able to abuse the wireless systems, seems like Pegasus got away with using a lot of them. Even without the virus, Pegasus should have been in trouble there. They can say they survived at the beginning because systems were down, but why they were able to fight a running battle for months after that (and before they purged the virus from their mainframe and vipers) is a rather gaping plot hole...
Dialoge in "Razor" explains that they never installed the CNP with the virus in it at Scorpia, which is why the ship survived the ambush. Later, Pegasus Six was able to partially infiltrate the system using the command codes she'd been given. After her capture, presumedly they simply purged the affected systems and reinstalled the non-virus software.