[Rojma]

I was surprised the Admiral didn't make any mention of what Pegasus did to overcome the Cylon attack on the networked battlestar computers.

I'm betting that they use just that to disable the Peagus and get back the Galactica crew members. They could use the Cylon aboard Galactica (Sharon) to spread the Cylon virus to the Peagus, disabling it and all of its fighters giving Galactica the edge. I'm sure Sharon would be more than willing after her attempted rape.