(or bigger ones, but not requiring one to get through several floors of different buildings)
The aforementioned goggles do half of your work for you on such missions. The other half?
Shooting them through the walls with EM rifles (bolters) or if you really want, coilguns.
As for saving the civilians, if the aliens can see/shoot only civilians, that's wh they will kill.
If you just winged said alien (for maybe 1% of his health) with a laser pistol/rifle, and they can see you behind partial cover, they will often target you first.
The same holds true to a lesser extent if they can see an ARMED phalanx soldier (they will often ignore zero items carried fodder).
Unfortunately, sometimes saving the civvies means giving the aliens soldiers to shoot at. Also, yes, some maps, there are civvies that are just too dumb or badly placed to live. The trick is figuring out HOW exposed you can let your soldiers be without them getting killed.