Alpha Protocol focuses on the paramilitary side of the espionage house. But think about it. Real espionage is akin to digging through a pile of **** and trying to find a diamond; pretty much what Parker does. Many people would find that boring, hence the emphasis on field work. At least that's how I see it. As for reptitive (sp?) takedowns... there are only a handful of ways to KO/Kill and enemy without making a ****load of noise, so being reptitive (sp?) is unavoidable.
You can also buy a silence for the pistol and mix it up a little.