Well, I prefer to leave the Command as NPC's.  Essentially they will give missions and rules of engagement...

https://en.wikipedia.org/wiki/United_States_Marine_Corps_Force_Reconnaissance#Creed
This Creed should give a good idea how far they will go.
Civilians will have SOME say in matters, but really as experts and mission needs.  But if command says they are not expendable - you will have to make the decisions regarding risk.  If they get unruly ... well, the mission success comes first.

In other words - Boots on the ground get to determine how it goes down.  This is why I prefer the military be Players.  I DO have a gunnery sergeant I plan to use.  He is VERY young for his rank, but earned every bit of it.  His nickname is "Airsoft."  He made the mistake of admitting he had played the game during his FR training.

The OTHER positions are a couple of civilians.  One is the Gunnery sergeant's younger brother and wife.  They are fully competent though.  The brother is a former marine who tried to make it through FR training and didn't make it.  He became a mercenary asset for the CIA.  He was just not the hero's hero that most force recon are.  His main asset was his brains.

Early missions will be purely recon with few civilians in tow.  The main missions will be to locate human survivors and see what has become of civilization.  Side missions will include CBR type samples of the ecology to see how the war affected things.

The early missions are pretty self explanatory as the teams will soon discover signs of civilization.  

Edit:  Mostly I ant to keep my mucking by CO's to a minimum.  Unless there are incidents with misbehavior, of course.  (Like some civilian whining ... then maybe a review board later).

The civilians should be professionals.  They would be the sort of people you'd collect as experts in TV shows like Threshold, or movies like Andromeda Strain or Arrival.  They didn't quite get the best as they had other factors as well, like age and sex ratio.  (It turns out that 50 people is the dead minimum to restart civilization.)  

I am not dead set of the number 50 either.  But they had to be fast.  Even in 2019 we are close to fielding hypersonic ICBM's.  This is the reason they collected everyone as soon as it looked like the war would go hot.