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Your party has infiltrated deep into hostile territory via a magical portal. Your current objective is located in a fort hosting a garrison which is used to control and terrorize the local village and area. You have already defeated the garrison, but a majority of them have miraculously staved off death and are instead scattered throughout the fort unconscious. Achieving your current objective will close the portal you came here through, and your next objective is several days away deeper into hostile territory. Reinforcements from other forts are likely on their way.
What does your mostly good party do with the surviving garrison?
Get out of Dodge and leave the garrison as is. If reinforcements are on their way already then they've lost surprise, there's not an amazing amount of info the survivors can tell that a good investigator couldn't find out anyway. Just the PCs descriptions really (use disguise or similar).
Killing the garrison will neither prevent it being restaffed nor make their replacements better people.