I like your take on why the primary drama was diverted and shall adopt it wholesale (hee). I do hope that it will serve the greater good/history for the rest of the season and that this plot point rears its head again.

Regarding the raider, as it was approaching Galactica and then landing, I was thinking about all the destruction that one small beacon did to the Cylon basestar in the previous episodes! I was completely expecting the Cylons to reciprocate with their own viral Trojan Horse and was surprised that Bulldog wasn't infected with bubonic plague or some such disease.