Actually this is a great idea.
There is a huge scope for imagination. Here are a few ideas of how helping the neutral NPC fleet might end up
1. Quest for researching the system: "Hey, thanks for saving the fleet of my rusty cans, I'm in your indebted debt. But perhaps right now I have nothing to thank you, although I can share with you the coordinates of the cache where I hid a little (specify what you need - resources /weapon/artifacts of the domain era")
2. Quest to eliminate the target: "Comrade Captain, I thank you for helping my civilian fleet, without you we could not fight back. But I know who is behind all these assassination attempts - this is the same malicious pirate (insert name) who wants to crush all trade in the sector. If you want to help not only me but all the merchant fleets in the sector, go to the system (insert the desired name) and meet in the bar on the planet (insert name) with one of my good friends who knows where to look for this brutal pirate."
On the planet, an NPC is waiting for us, which issues a quest to eliminate a unique pirate, with a unique ship or weapon.
3. Escort quest: "In the name of the holy Ludd! Your name will be recorded in all the chronicles of history! Please escort us to the system (insert name) to the planet (insert name) and you will receive half the profit from the sale of goods that we carry on extremely profitable market"