Hey - speaking from personal experience, the best way to resolve this is to have a healthy dialogue with the players involved. Discovery is all about sandcastles, and I don't think you did it intentionally, but you stepped on a few. There's nothing wrong about that, and it's quite inevitable if you want to play anything other than a boring, inoffensive, and stagnant faction.
With regards to Rheinland (which I've observed directly) - you were caught working with groups that have enemies (IE: corsairs are universally hated in Rheinland, Hessians are universally hated by Rheinland lawfuls except for a weird ceasefire relationship with the Feds, and Kruger/Daumann miners which are at war with the Feds and the Hessians). None of that is inherently wrong, but it was motivation enough for the Federalists to be suspicious and ask for an explanation and want the FTP to stop working with groups that they are at war with. Apparently some FTP characters were rude to some BDM| and KAM characters in space which is totally fine and good, but would also inRP not help the situation. After diplomacy went down (FTP was offered a working relationship with the Federalists through the BDM| for a time, but the FTP withdrew), there was no choice for the Federalists but to assume that the FTP was working with the hostile groups that they were found with, and that made them targets.
That's inRP - OORP wise, I recognize FTP is a new and very motivated group of players, and I'm more than willing to work with you guys to find out what you want to do - and we can discuss what needs to be done so that FTP and the Federalists don't have an inRP reason to shoot one another.
With regards to the base sieging, I can't really speak to anything other than that O55 is in the back yard of SCRA/Hessian/Corsair country - and given that two are terrorist space communists and the third is a food pirate empire - so they're not the cuddliest bunch.
