If the goal is to discourage the party from doing such things, here are some ideas that might help:
1) In combat, have some enemies spend actions rousing/healing fallen companions to get them back on their feet. Having a consequence to leaving enemies alive may make the party less inclined to do so automatically.
2) What is the party doing with enemies after questioning them? If the enemy cooperates and the party let's them go... perhaps make a point of having that come back to haunt them. Perhaps the enemy goes on to threaten them again - or, worse, causes harm elsewhere and the party is blamed for letting them go. Or, if you want to avoid making the party feel quite so bad, you can instead go with the 'nuisance' approach: After being defeated by the party, many enemies become obsessed with them and swear 'loyalty', and then spend all their time following the party around and constantly being annoying and in the way.
3) Or, if the party routinely kills the enemies during questioning... what are the laws of the kingdom, if they are traveling within one? Defeating an enemy in battle might be one thing, but torturing and killing them afterwards might be different. Even if this is allowed - perhaps because the enemies being killed are monstrous creatures, for example - it might still get the party a darker reputation than they want. Maybe some of the fallen have families or clans that take offense to how they died, and come after the party for justice or revenge?