Because they kill your people when they invade and siege. Then when you avenge their woeful acts, you take them prisoner!

Bull, its just bad programming and a bad design. Why should my army that stands on guard over my own people see an entire pop die before they take prisoners of war. I don't need more slaves in my capital.

This is a bad design.

ok, tell it to Reader's Digest.

It may be that bad programming ended up being just more accurate historically: an ancient army recovering a lost province was not the Allies freeing France in WWII...
It was the norm to exact "punishment" on the unfortunate inhabitants of reconquered provinces and in general terms the ruling elites (even republics were the expression of a small elite) had no qualms about killing or enslaving their own citizens if felt them being not loyal enough, and being occupied by an enemy was seen as an excellent reason for collective punishment: afterall if they were neither killed nor sold as slaves the only reason was them being traitorous scum.
Sure, a plump and timely tribute (and a quick cleanup of the ruling class...) could avoid the worst but that's all.

Just an example: in the year of four emperors Cremona (a roman colony in northern Italy, whit full roman citizenship) was occupied by units from the army of the Rhine loyal to Vitellius.
These units were defeated by troops loyal to Vespasian which after the battle looted and burned Cremona to the ground and enslaved its inhabitants.
As they were Roman citizen this proved to be quite embarassing for their commander, who (note the wording...) forbade his soldier to keep roman citizen as slaves: as a result the soldiers murdered the unfortunate citizens.