What fleet are you using that can kill the huge ordos but not the station? Also, what is the point of allying with pirates? The remnants will kill any fleets that try to raid you. That seems like the main benefit of settling in an active remnants system to me. I've done it in a medium threat system before, and it worked very well for letting me get my defenses set up slowly without worrying about raids.
3 Legions the special ones you find, full spark wings, 2 Apogee (1 I stared with) 10 Drovers full spark wings, 3 Eagles and basically everything I can get my hands on. Fighters are great at smashing the fleets but terrible at fighting a Ordos station.
Basically send in the carriers first, set a single rally point to the center back (Literally on the line closest as you can to the re-enforcement point) to clump them up. Once the enemy starts pushing past the fighters which weaken and kill the smaller ships, you start sending in the fighting ship as needed to push back and finish off the Battleships/Cruisers. The ships being so far back means an easier retreat if things go wrong and the fighting ships can get in Battleships face ASAP. None of those fighting ships can beat the larger Ordos stuff but they can finish off ones the fighters can't bring down.
Everything about this strategy working depends on being able to retreat and re-enforce fast. Sparks are a 100% requirement for this to work, other fighters can't handle them. So you need to farm them from medium systems long before trying this. If a Ordos battleship breaches the fighter line without a real fighting ship in it's face with more then 25% flux for even 5 seconds your losses will be terrible, a Drover dies in about 2 seconds. The cascade of lost fighters will cause more breaches.
It's all or nothing.
edit 2:
Missed the pirate point. Because the pirates are the best trading partners, they can resupply every shortage if you are on good terms with them. It also means when I wipe out the core and/or it dies I still have a trading partner. Neutral faction is nice but will never help you on the battlefield against the major factions, the Pirates will.
There are other HUGE bonuses people overlook that makes up for the lack of commission. I can sell all Blueprints directly on the black market without paying 30% tariffs losing 150,000 of a 500,000 blueprint and fearing the Pirates gaining access to new ships. I mean the Pirates in my game have Astrals and Paragons lol. If they are my allies I WANT them to have better ships. Hell I gave the Pirates a Pristine Nanoforge, I mean I got 6 just sitting around doing nothing so why not.
Update:
The station has been brought down by 8 allied fleets in a single battle. I have a fully upgraded planet, Starworks(with Pristine Nanoforge) and Military command.
I don't think thats true? Could be wrong, but I've never noticed any scaling.
It felt true, but fighting about 200 fleets total was fatiguing. I didn't see fleets with 3 battleships till many kills in. I know for sure probes defenses get stronger the more you destroy, but for the Ordos my experience is anecdotal as I wasn't recording the fleet details.
If they did get stronger it was 1-2 bigger ships at most. Battleships seemed more common later in. I don't recalls seeing a 4 Battleship fleet, but it's a giant blur at this point.
edit:
Ordos fleets completely ignored Tri-Tachyon and even aided them in combat when cross faction fighting took place. It's on the wiki that they are allies but it was funny to see.