Need to kill everyone on map to save Helena?
Don´t like attacking possible allies.
You will sometimes have to do this, but often such story missions don’t decrease your standing with a faction or do this in small amount.
Play hard-ball to save humanity, eh … ?
yep. Game don’t have enough choices in this regards yet. I hope it will change with time. But devs first need to deploy other stuff which was planned before making game more diverse.