It's not unreasonable for the Lucian Alliance to be a threat despite the technological differences.
I think the explanation is that while SGC has been collecting/deciphering Asgard/Ancient technology, the LA has been similarly scavenging technology from dead System Lords (Anubis/Baal/whatever)
Given the speed of hyperspace in the Stargate 'universe', it makes defending any planet virtually impossible. They showed how one of the attacks could go in Season 2. The only problem with their plan was they wanted the pilot to survive. Hard to defend against a cloaked ship with a bomb.