Sounds like a similar problem to Bioware’s KOTOR, where the light choice on the wookie planet is not to kill every single slaver piece of garbage you meet until the end. Also has an additional outsider savior narrative (not strictly white since your character has a lot of race options) where the wookies don’t even seem to seriously consider just killing the sith until you come by and are all like “hey what if you just killed the sith.”
Both Obsidian and Bioware are good at making games that respect player choice, which often leads to them fumbling when it comes to tackling politics. The difference is that Bioware often weasels out of the real world implications or just uses it for set dressing so not to distract from the big bad and maybe evil thing (depending on the game) coming to do a genocide or omnicide. Obsidian tries to engage with political ideologies, resulting in a spotty record due to how uneven they are when it comes to denouncing things. They do it a lot, but respecting player choice so much can undermine the themes at play.
Alpha Protocol probably has this worse because you can side with the most nakedly evil faction in the game, the one based VERY much in real world politics the developers clearly despise. The game makes it clear is is a genuinely evil choice, but Thorton is still shown off as a cool guy (but now bad) so it doesn’t really gel with the core message about the evils of arms dealers, political corruption, and capitalism run amok.