AI for civilians and for aliens is different.
I am not 100% sure about the details (so this entire post may be somewhat inaccurate), but in vanilla OXC (and the original game), aliens only react to civilians in their own turn. They don't reaction fire at civilians, ever. This was fine for vanilla, as it allowed the aliens to preserve TUs to fight X-Com instead of spending it all on wandering civilians.
However, with introduction of armed civilians, the situation got complicated. The aliens kept ignoring civilians to a degree (to preserve vanilla behaviour), but this gave armed civilians an edge against the aliens. To make it more fair, Warboy decided that armed civilians would not reaction fire at all. This indeed made it more fair, but also made alien-civilian combat asymmetrical.
The solution would be to 1) give civilians the same AI as aliens, and 2) make aliens react to armed civilians like they do to X-Com, and to unarmed civilians the same way as before. Meridian expressed interest in adding this to OXCE+, but it hasn't happened yet and I don't know when - or if - it will happen.
I agree it is a bit of a problem now, since I also have military "civilians" in XCF... They are mowed down by pretty much anything.