If his family really is under witness protection, Samantha wouldn't be answering the door like that for the neighbor without MC around.
Didn't want to go on a rant about the whole witness protection thing, but here I go. The main problem with the witsec premise, is that people in witsec do not have private security assigned to them. Ever. The whole point of witsec is to give new identities, and move them across the country, where they can blend in and lay low until it's safe(if ever) to return to their normal life.
People in witsec have a government agent assigned to be their handler. That agent will be available to call in an emergency, and will keep an ear out for possible security risks, like the suspect escaping custody. That agent will -not- live with their protectee(s), as that would be very weird and would make blending in and laying low very difficult.
Most people in witsec will have a normal job, and have to provide for their own rent, bills, food, etc. Receiving a "salary" as it was called in this game, is only ever done in situations where the protectee cannot safely blend in anywhere, and thus cannot go outside, such as with famous celebrities.
Edit: Forgot this major point. People in witsec, as I mentioned above, get -new identities-, so MC calling out to each of them by their real names, in the middle of the street, would automatically have them moved to a new city.
As a veteran, I'm not even going to go into how ridiculous the military stuff in the game is. Someone else already covered it pretty well anyway.
My best advice is to just treat it as a cheesy porn plot, and do not take any of it too seriously. I'm one of the weirdos that mostly plays these for the story, so I definitely prefer when devs stick to writing about things they actually know, or at least do some actual research, but this one had me laughing pretty well, and I actually enjoyed it once I turned my brain off and just accepted it for what it is.