I think we can agree that that's another instance of 'blowing up their stuff'. Let's come back to 'what is the consequence of negative reputation within the mission system?'.
In my opinion the negative axis of the reputation scale is going to be under-utilised in the new Engineers mission board, because none of your actions need have the result of creating a negative reputation with a faction you have to interact with.
In other words, picking a side has no consequences. If you choose to bounty hunt or attack a surface base belonging to an arbitrary faction, repeatedly, you will go negative with them, but then you just won't get missions from that faction. The same sort of missions or better will be available from similar factions in similar economies elsewhere. You will (once any Wanted status expires) be able to dock at their stations, but they won't attack you on sight, send hitpersons after you, their authority vessels won't target you for interdiction and scans, they won't withhold any unique commodity or resource from you.
What I'd like to see is a choice where you do something to advance A's interests which reduces your standing by an almost equal amount with B, and at some point you will need something back from B so you may have to start trading to them, doing menial missions or even attacking A's ships.
Examples:
- Faction B controls the only Commodities Market where a Rare good is sold
- Faction B controls a station with a Black Market and only allows access to it with Cordial or better rep
- Faction B controls a Shipyard with a good selection of ships
- Faction B controls a large pop High Tech station with a great Outfitting range
- Faction B controls access to an Engineer
- Faction B controls a permit system where a rare Material can be reliably found
- Faction B can call off hitmen from an opposing powerplay faction.
Factions have a set of assets like systems and stations but also by the other items that they could gate access to based on Reputation. This gives them a sort of 'market capitalisation' which then should affect the value of missions performed against them. Supply and Demand, if you like A mission to attack or smuggle past a powerful, large faction B with some of the above assets should well. Faction B, on the other hand, can afford to pay comparatively badly to harass the weakling Poor Agricultural Faction A nearby.
So if you want a big payout quickly to afford that big ship, you might have to take missions that will annoy the big fish in the neighbourhood.
