How was this assumed?
Recently, I have been running into an issue with an ultra-high fire-rate weapon within a WIP module. It appears to make factions hostile extremely quickly, even with accidental fire. Each projectile deals very little damage on their own, but many projectiles appear to cause hostility rather than damage dealt.
How to fix
Alter faction reputation logic to deduct reputation based on total damage dealt to faction ships instead of total times hit
Potential downsides
The most obvious downside I can think of to implementing this change is allowing the player to fire at allies for extended periods of time using low DPS weapons. While depending on context this could be unrealistic, I would argue that making high fire-rate weapons risky to use in front of allies is a bigger downside.