Not sure if I'm still in chapter 1, (how big are the chapters?) but the squad is talking right after first meeting Safiya, talking about Grace. My one big problem is killing your own assets as a first move due to exposure is shitty SOP; even, or especially, for espionage assets you should go with an exfil over an assassination, unless you're both lazy and cruel. Grace, reportedly, just arrived on planet, move her to a different part of the planet or a completely new one. Trade her as a favour to a different org. Killing her is a waste, and the way it's treated as no big thing (especially by Elise) really bugs me.
Also, the Officer should really start using his commander status soon, like keeping Aria, who is outside the command structure, away from their base. It's all very messy.
The one year timeline also stretches plausibility, but I've mostly come to grips with that. Game is very good though, understanding the hype.