So… a confession. I've worked on Alpha Protocol for almost 2 years, and I don't know which characters are good or bad. Which, in the spy genre, is a plus.
They all have their reasons and agendas that don't break down neatly into good and evil. That's fine; Obsidian's already worked with the Dark Side/Light Side range (Star Wars: Knights of the Old Republic II: The Sith Lords) and also juggled the spectrum of Dungeons and Dragons alignments (Neverwinter Nights 2, Mask of the Betrayer), so diving into murky moral grey areas was a nice change of pace. Also, it was kind of liberating to just have the player do things, with the world reacting, and leaving the results up to cause and effect.
In Alpha Protocol, the cause and effect breaks down into your objective, the means, the results, and then someone's reaction (and the results/reactions usually spur different objectives, and… and well, the vicious cycle continues). In short, the way you treat someone sends ripples outwards, and others agents and figures in the espionage community may either disapprove of your methods (loudly or quietly or with a fake smile as they're slowly drawing the gun from their jacket), or they may like the fact you stomped over someone to get where you needed to go. Even your bitterest rivals may respect the fact that you keep your mission in mind… no matter how many of your allies lie dead on the battlefield once you leave.