Right now if you are in sector, and having your NPC controlled fleet aid an allied fleet or station, it is likely that friendly fire will occur turning your allies hostile.
Could this be disabled somehow?
1. Disable damage to allies, they will not turn hostile.
2. Damage remains, but unless targeted, allies will not turn hostile.
3. Damage remains, you are required to visit the faction representative within x time to pay for damages caused or face hostile relations.