History lesson: The Republic of Dublin has a very, very good reason to despise BMM's corporate overlords.
However, ideology gives way to pragmatism after a certain point. They'd probably be willing to negotiate a settlement of a large sum of credits, docking access, and other sundries (mostly political in nature), but you had to essentially say "Hey de facto dominant power in Dublin, I'm not going to let you in." The expected is happening.
At this point, they've committed, but your response to their completely reasonable "we're the big bad scary taxation-leveling unlawfuls, and we're working our way up to asking you for a contribution to our glorious cause" could be summed up as a restatement of BMM's corporate policy. That is not something they want to hear.
If I were you, I'd call the Mollys back up and apologize to them, citing that you were talking to Gauls or something and got a wire crossed. Both sides of the table know it's a lie, but it's clearly to save face. Just pay their base fees. You'll make your money back in two runs, tops.
Well, no. I am obligated by the rules to not let enemies of Bretonia dock at the base. Mabye a bribe could have worked, but the Mollies keep pestering us for a few days anyway. The base is remote, so no harm done for Molly patrols either. If they want to be the dagger in the backbone of Bretonias economy during wartime, so be it. Even bought a Battleship for the occasion, so hopefully they don't bring in the Gauls or the corsairs //and I am not at work or sleeping.
By that interpretation of the rules, one could claim to be obligated by the rules to not cooperate with the pirate whilst on a corporate ID. Ask yourself in-character whilst on your unarmed 5ker "How do I get out of this alive/with as little lost as possible?" That big scary ship with the ability to turn you into scrap is willing to not turn you into scrap in exchange for a portion of your profits.
The pirates don't want to discourage activity, so they will be reasonable. Especially considering that this is coming from an Official Faction. Just talk to them and be civil.