Like it is now, it only reflects in the amount of skill points in the ending of mission. That should be revised and if player allow all civilians to be killed, or equipment to be destroyed, the mission should be a loss (even after kill all enemies).
Canny Official Feedback Tool topic:
https://feedback.phoenixpoint.info/feedback/p/give-more-importance-to-save-civilians-and-protect-equipment-in-haven-defences
Not even the SP is affected, but experience.
I have another remark here: enemies should not be placed so close to civilians, unless you have trained squad (a lot of invested in movement) or a dash ability, its often impossible to reach them at all.
You have a lot of nice proposals, but its way better to use official mechanicsm
to propose changes, and then present it here, so you might get voted to it.
Some people proposed that they try to pick weapons and defend, but with no armor, they are simply easy to kill.
I would prefer them at least trying to run towards your squad, instead current wait for rescue.
Thank you for the feedback rasvoja,
I write everything in Canny first, but like the community is here, this is the company oficial forums, and are more interaction i write everything here also. But you are right, i will provide the links of the same content i write in Canny also to be voted.
Anyway, like it is obvious, my goal is to give feedback for this great game become even better and a reference to the genre. It has potential to be a super game, but the late game with fantasy super overpowers at the moment turn it impossible.
I play this kind of games since 1990s and remember well the lap between 1999 (Jagged Alliance 2) and 2012 (XCOM Enemy Unknown) were almost no game of the genre (TBS Tactical Battles) appear and the ones who were created had lack of quality (exception to Silent Storm that was reasonable).
While I appreciate many great suggestions presented, very few have actually been included. Its more fixing critical bugs and unbalances, no matter the relative frequency of game updates.
I hope some good ideas are stored for PP2, I share your feeling that engine/innovation is great, but not used to full of its potential.
I will copy paste here all the links to Canny Official Tool editing each topic i created lately 
Thanks for suggestion!
Canny Official Feedback Tool topic:
https://feedback.phoenixpoint.info/feedback/p/give-more-importance-to-save-civilians-and-protect-equipment-in-haven-defences
The problem is that due to RNG, one may not have a chance to save the civilians or facilities, no matter what the defender does. On too many occasions all (or most) of the civilians/facilities are across the map, totally surrounded by Pandorans. To make matters worse 95+% of the time, the haven defenders do not get their first turn and are dead by turn 2.
Restarting helps a bit, but does not always help (randomizes map and spawning again).
To make matter worse, rescue soldiers suffer the same plague, minus limited ability of soldiers to defend themselves (often not enough).
Totally agree. This has been the case since the opening gate. The devs really need to address these and other long standing bugs. Yes, we know they are busy with the upcoming DLC and trying to placate those that want a more realistic (and less fantasy TBS game). But, the long standing bugs and issues give the appearance of shoddy dev work.
I totally agree, but neither should be preferred over the other. Fixing bugs is certainly important, but also good balancing and further development of the entire including DLCs.
But, according to some they aren’t doing either.
Well, most of most annoying bugs have been fixed. Now it needs “finetuning”.
Like restoring badly damaged car to a really polished state 
Hope after the DLC some new “directions” will be seen.