I don't think Nova Imperium was the best example there, I doubt the League of Mandu have ever felt the need to establish their own military to protect against the Federal Navy coming to execute them all.Where in the article does the Federation endorse the League of Mandu's invasion, and where is Admiral Natalia Lee identified as a member of the Federal Navy? Minor factions have their own private military/security forces (example: Nova Imperium).
All the evidence points at this being a Federally-sponsored attack. Sure, it doesn't explicitly spell out who is backing the Federal Admiral, commanding a Federal military (Well, it does in the headline, but we're ignoring that). It also doesn't spell out how such a small faction got the resources to launch a massive military incursion far from home with a military megaship - maybe it was the Federation? They were actively demanding a response to the leaked intel, and its weird how they haven't yet been denounced if they're really not there with the support of the Federation.