Another though that clattered around my head, found nothing to latch onto, and flew out:
How about a script that, for players (and this is the important bit) with reputation 0 at the minimum, adds a single reputation point at the end of an encounter for each NPC belonging to a particular faction still standing (or simply for the entire group if the gain for each NPC works out to be too much) - of course, only if the combat ends through "End Combat" rather than grid exit.
To avoid "build up then drop" approach, I guess another flag would be required that would mark a player as non-hostile, or hostile if any such attempt was taken against a particular faction. For any character with the hostile flag toggled, no reputation gain through this mechanism would occur.
Also, perhaps it would be possible to pay a substantial caps amount (or make a trade of items for the given value) to clear the flag - basically, paying "blood" money, and only within a limited negative reputation threshold (-199 upwards?). Again, this amount would be very large to avoid exploitation and make it simply a viable option for somebody with true vested interest in maintaining good standing with a faction regardless of a chance occurrence (for instance, despite having never attacked Regulator patrols in random encounters, a single miss shot during an encounter with a thief dropped me to -125 with them).
It would allow a hon-hostile (to a particular faction) character to build up reputation with factions that may not be considered interesting trading choices. Since the gain is pretty small, and any hostile action would result in loss of such gains until the matter is addressed as described above, it would also require the character to maintain non-hostile approach to a faction for a prolonged period of time.
The reasoning behind this, in "in character" terms, is that through continuous display of good faith a person would gain reputation for being a trustworthy (or at least, non-violent toward a particular faction) person. Since "other people" (NPCs) met during the encounters survived to spread the word, it would be simply a matter of time before one is known for their non-hostile stance.
I'm positive the details would require tweaking to avoid exploitation, but also convinced that with care such a system would be a valuable addition to the current reputation system.
tl:dr version: people killing NPCs get loot and exp. People not killing NPCs, under certain strict conditions, would receive miniscule reputation gain with the represented faction.
