If Palazzo wishes to expand upon or conquer Malignatus, that is a matter left to his own abilities. But the might of the Fleet will protect the Nobility of any House, when attempting to escape a battle they cannot hope to win.
Why is the Fleet interfering now?
Really, right now, both sides want to fight, and this is of no concern to anybody else.
Because you changed the situation. Let me break down what's happened here.
-I'm appointed Fleetmaster, and promise to enforce some semblance of "law" by using the Fleet to punish acts of all out war. This is hampered because the Fleet has to rely on everyone else telling it where units are, because I can't see anything.
-You landed some dorks on Malignatus at some point between the last 5 and 30 turns. I was unaware.
-Mainiac moves to kick you off the planet. I say leave nobles out of it. He attacks said nobles, admittedly with weapons that couldn't hurt nobles, but I never risk my nobles in combat so I didn't know Nova doesn't let them get hurt anyway.*
-I fire on Maniac's forces around the noble, and said you could send some transports to remove him. I say war is war, but let's try to maintain some kind of civility.
-You took my allowance of a rearguard to evacuate the noble as an excuse to land an invasion force. While war is fine, this was still a gross disregard of the (my) rules. The rapidly escalating scale of the problem leads me to declare that any further shipping activity is hereby off limits, and that you'll just have to fight with what you have.
Now I'm sitting in the awkward position of actually enforcing that. Yes, it's clear that wars will be wars, and allowance must be made for conflict. So my rules are a bit untenable. However, there is the more temporal problem that you, Palazzo, started this dust-up in violation of my warnings at the time, but I only got the chance to actually damage mainiac. Civility does include some sense of fairness.
*EDIT: Actually, I looked back the saves, and Palazzo's noble was a Blademaster. Having actual combat stats, like a Close ability, can't they be damaged by any kind of offensive unit then?