I've been playing around with combat missions, basically just throwing myself at random combat missions and then resetting to get all my starter money back, and I only just realized something extremely useful. The overload tool you use (default binding is to 4) to open doors or power terminals can also be used to take down enemies with shields or armor (not sure which it is that causes it) stealthily.
If you sneak up behind a guard patrolling with the power tool out and set to the overload mode, you can overload their suit and insta-kill them without setting off any alarms. You will still gain a bounty for murder (not sure if this is intentional or a bug due to alpha) but you can eliminate some of the tougher outside guards this way if you haven't bought any of the upgraded suit or weapons yet.
From what I can tell this doesn't seem to work on the scientist NPCs who are inside certain areas. My guess is because they're not wearing armor so the overload tool doesn't have any effect. I have yet to find a decent way to kill them without triggering the entire settlement yet. I'm going to try some variations of melee to see if that could work, but at least this can help you reduce the heavily shielded guards that are around in case shit goes south.
Not sure how many people were aware of this feature, so hope this post helps some others at taking down some of the more powerful guards when trying to finish missions.