What does a person need a structure planet killer for anyway? The player flies fighter craft, which in and of themselves wouldn't do a damn thing to the Shadow Cloud. In my opinion anyway, the Shadow Cloud from Into the Fire and A Call to Arms are two different beasts. Really, the League fleet in ItF is surrounded by the cloud and no one notices this huge structure framework?
You can do the mission from ActA, just have the player flying around, doing very little while hordes of ships are blown up all around him and the Victory fires at some point out of sight and suddenly the player wins the mission. That's about how effective the player's going to be in that sort of scenario.
A far more interesting scenario would have the player trying to stop the Drahk ships from releasing the plague while the EA fleet of doom goes and does their business. Because really, what would the player being doing in that scenario which would be of any use to anyone? Even if they're protecting the Victory or its sister ship, just have them flying close escort inside some black nebula. With the occasional slow moving missile to shoot down or some Drahk ships to itnercept or whatever.