This is an overview of the reputation changes introduced in the build 9 scenario update.
This post will not reflect any changes made in later updates. See the Change Notes for info on later updates.

Reputation changes:
The reputation system has been overhauled.

If you looted a container, harvested a crop, killed an NPC, or destroyed a block you would instantly drop to neutral reputation regardless of what reputation you were at.
This could be very punishing for players with high reputation if you accidentally shoot a trader in the face, or a stray shot blows up a piece of fence or hits a friendly drone. You'd instantly drop from full honored to barely neutral.
Likewise it also opened up cheesy tactics since it allowed you to loot ultra rare containers or destroy cores with minimal reputation loss if you were just slightly into neutral reputation, then easily regain your reputation to do it again.

You no longer get reduced to a specific reputation threshhold. Instead all actions have a flat reputation penalty assigned to them.
The difference is that mistakes are less punishing at high reputation and more punishing at low reputation. Accidentally shooting a target now has a much lower chance of wiping out all your reputation if you were friendly or honored, though you should still put away your shotgun before speaking with a trader.

• Removed all threshold reputation losses (losses that resulted in your reputation lowering to a specific reputation level regardless of what level it's currently at). All reputation losses are now flat amounts based on action taken.
  
• Removed passive reputation gains while outside of a territory.
  
• Attacking a NPC or shielded structure will lower your reputation based on the damage dealt.
  
• Reputation losses while inside faction territories from actions such as mining ore, harvesting plants, destroying plants, spawning structures, remaining inside a territory in a ship, and killing prey or predators will still apply based on the faction and are largely unchanged. See the in-game faction info window for details on a per-faction basis.
  
• Killing a NPC will drop your reputation by 1/6th of a level (-1000). Note that sentinel NPCs do not tolerate violence and will open fire on you and kick you out of their base if they personally witnessed you attacking an ally even if you are still friendly with them.
  
• Opening a container or harvesting a crop will drop your reputation by a full level (-6000).
  
• Destroying a block will drop your reputation by 1/20th of a level (-300).
  
• Destroying a generator, fuel tank, thruster, spawner, or turret will drop your reputation by a full level (-6000).
  
• Destroying a container will drop your reputation by slightly over a full level (-6600).
  
• Destroying a door will drop your reputation by two full levels (-12000).
  
• Destroying a core will drop your reputation to full hated (-30000).
  
• Removed Kriel reputation. Kriel is now a default hostile faction.
  
• Removed explosion effect from decorative shuttles so that if they impact a POI it looks like they entered it instead of flying to their doom.
  
• Added Icon of the Brotherhood decorative block for POI decoration and future mission or trader rewards. (Thanks to Spanj)
  
• Updated refinery defense combat site. Increased shield hp and recharge rate for refinery. Updated defense ships to RE2 version. Added self destruct to defense ships to prevent cluttering on MP. Various tweaks to the mission.