Seems like you spook civilians whenever you walk by them, is there a way to hide weapons to appear less aggressive?
There is no way to holster/hide weapons as far as I can tell (and I've tried a variety of button combinations and holding different buttons... no dice). The best thing I could find to do was to keep some distance. They don't really seem to notice you or scare away if you stay a short distance away (20-ish feet maybe? That's a complete guess, but probably not far off).
However, scaring them does not seem to have any negative consequences apart from triggering negative dialog directed at your character.
And as you mention in a comment on another answer, there are some civilians that need aid and will give you XP and sometimes a random cosmetic item. They will look more sickly than most other civilians and will appear to be scanned by you. These civilians will not react negatively when you get close.
I find that when you approach them head-on, you get a higher chance of scanning the sickly civilian and getting the Aid Civilian prompt to pop up. Once you aid them, there is from what I can tell a ~5 minute or so timer until you can aid another one.. From my experience, they drop cosmetic gear 75% of the time, worn / grey items for dismantling 25% of the time.. There is also a corresponding sound when you begin to scan them, so keep your ears open.. Also once scanned you only have a short window to help the, before they get snotty and walk off upset - a few times I was a second too slow and lost my item but got no XP or reward. Hope that helps.