Killing a Highkeep guard should never lower Freeport militia faction if the guard you are killing is named (for example, "Guard Bach"). Only the mobs simply named "a guard" share Freeport Militia faction with Highkeep faction. The "a guard" mobs look exactly like Highkeep guards and can be found on the second floor.
It is currently working as intended. I hope you didn't change factions based on a stupid thread where the OP clearly doesn't know shit.
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