You know the main problem? At the end of the day, you still want to simplify the game down to two endings: Work with the Baron or work against the Baron. And you make the Baron the "evil" side apparently.
I know you want a complex morality system, but I argue for a complex FACTION system instead. Instead of having 4 different traits, have your relationships with certain Factions go up and down. So:
---Baron Villian
---Thomas Bartender
---Priest Buffalo
---Joe Trader
---Jim Banker
Etc. And each of these people hand you missions. Completing these missions will increase your relationship with one of the guys, having you unlock more missions from that guy. But it will likely also offend another Faction. Angry factions will respond to you rather negatively. In the end, if you make that faction too angry, they'll refuse to talk to you and will instead send their goons to attack you.
For example, say Joe Trader gives you a mission to shut down some of Baron Villian's henchmen. Pulling that off makes Baron Villian upset and cut off all contact with you and send off his goons to hamper you. You can then petition for Baron Villian to stop attacking you and give you more missions, and Baron Villian will want you to "prove" your new-founded loyalty by having you attack Joe Trader, offending Joe Trader. But, of course, to prevent people from switching sides on a whim, it should be hard to get in the good graces of a person who hates your guts.
At the end of the game, the tensions between the various factions explode, with at least some factions wanting to remove the sheriff in question, and a civil war is going to occur with the "Pro-Sheriff" factions fighting against the Anti-Sheriff factions. So, if Baron Villian loves you, you'll end up working on the same side as him. If Baron Villian hates you, you have to fight him. Same with all the other factions. If, at the end of the civil war, you still survive, you...um...er...win! Good luck cleaning up the bloodstains.
If you somehow make all the factions like you, you get a "YOU WIN!" screen and prevent said civil war (this may very well be the conventional "good" ending, where bloodshed is avoided). Alternatively, if ALL the factions hate you, get ready to inflict bloody massacre onto the entire Town that will make Baron Villian look...well...like a Hero (hence, the conventional "bad" ending).