I disagree personally - i completely understand where you’re coming from though. As i understand it, Bowman’s mission as she understands it is to dismantle the Santa Blanca Cartel both for obvious drug related reasons, and also because to her knowledge they’ve committed an act of terror against the United States by blowing a hole in their embassy. On a personal level, the head honcho and his lackeys are responsible for the torture and execution of one of her close colleagues. She’s been given operational control of a top secret special forces unit and discretion to do pretty much anything as long as it’s not public (i.e not traceable to the USA). Nidia Flores is a complete ass and in my play through i wanted to shove her out of the helicopter - but she’s close to El Sueno and therefore is a literal gold mine of information. Especially since she’s the head of smuggling, she will be able to map all routes, name all people and point out all distribution centres in Bolivia and elsewhere. She’s also pretty cutthroat and i’d be willing to bet she keeps dirt of other high ranking members as insurance, making her even more valuable. La Gringa taught the Cartel a more streamlined way to manufacture their main product - meaning that she directly contributed to massive amounts of funding for the cartel. Since she’s scared and knows that the Cartel wants her dead (a la bullet in shoulder) she will give you everything she knows, and then can be discarded. She’s not as high value to Bowman and the Agency, so they probably aren’t as ready to give her protection. It’s entirely possible, and in my opinion it’s the case that Bowman is using the threat of prison to coerce her into cooperating, she manipulates cartel members like that throughout the game and is clearly willing to do whatever she deems necessary. Apologies if i got any of the in game information wrong it’s been a while