I only played the some of the first Splinter Cell and then Chaos Theory (number three). In the original Splinter Cell, Fisher's tendency to torture was implied to be part of his loose-cannon Navy SEAL attitude: it wasn't Third Echelon policy to torture or necessarily allow for torture on the field, but it was tolerated as part of the slack on the leash that Third Echelon kept on Fisher. It also eased into the notion of torture as part of Fisher's approach: I think it was the third or fourth mission before Fisher actually snatched someone (a chauffeur, I believe) from out of the shadows and interrogated him while applying pain, and again, the implication was that Fisher was crossing into Third Echelon policy gray zone in doing so. Note that this was in 2002, so after 9/11, but before Abu Graib and the illegal combatants controversy
By Chaos Theory, Fisher was routinely strangleholding people (goodguys and badguys), during which the player could press info out of one and then choose whether to sleeper choke him unconscious or break his neck. (Now that I think about it, I don't remember a single female target of this process).
The normalization of enhanced interrogation of bystanders in Splinter Cell reminds me of the time when Nick was told by Todd Howard that in Skyrim, looting barrels took a higher priority to escaping the rageful rampage of fire-spitting flying dragons, not because it made sense but because it was an accepted convention in games like Skyrim.
(I tried to find the original bit, but it's not labeled in the episode indexes as Nick's Skyrim Story. But that same anecdote is referenced here.)
It could easily be that the grab-and-interrogate process became regarded as common practice by the Splinter Cell developers, only instead of just being stupid video game shit, it presented even less fortunate implications. I wonder if the US didn't develop a robust program for enhanced interrogation (including the numerous legal whitepapers justifying enhanced interrogation) if Conviction and Blacklist players wouldn't be twisting their knives into hapless victims today.
Also, Splinter Cell early on was about Fisher doing his day job. Somewhere around Double Agent I understand the series turns more political and melodramatic even introducing moral dilemmas and trust as a game mechanic. It's generally always a bad idea for an espionage field agent to get invested in his or her work, and Fisher needs to properly end his career as a burnt out drunk living the rest of his days in a special town for dangerous ex-spies.
Ironically, Third Echelon is a secret military branch of the NSA, who were regarded as the good guys until we discovered they're spying on all of us, treating us as suspects of terrorism (and handing evidence of other crimes over to the DoJ). And Fisher has worked over Americans before.