Rogues and Pirates decided to siege that base. They invited Commune and other Outcasts to aid them. Commune only has Outcast ID/ IFF but it is not indentified as a Maltese organisation, rather it is as a organisation who is... allied or related with Malta and it's people.
Commune had some bussines with Rogues, especialy with Alcatraz Rogues before we went a bit inactive. Commune also has huge interest in Manhattan, @Ryummel said what it is. K'Hara and Oracles also have their interest there, together with Commune as they work for one goal.
So what is going on? Nobody said K'Hara or Oracles will siege the base. It was said they will aid the situation so we could create a distraction for everyone, and buy us some time and insiders on Planet, to get closer to what we want.
On the end, I believe that K'Hara by it's ID isn't forced to shoot everyone they see. They can also ignore whom they want, right?
So why wouldn't K'Hara ignore Rogues and other pirates, while they siege base, and use the situation in their own will? Especialy if the said organisations, are in good relations with Commune and those organisations will respect (they do) for whom Commune works for?