I think Buffy was aware that Harmony and Spike were an item and she (Harmony) doesn't exactly 'run' away in Crush. More flounces off slowly while monologuing. But it's a general thing in S5, Buffy doesn't operate a simple stake on sight policy to any vamps. If they keep out of her way and don't come snarling up and game facing at her she doesn't seek them out. If they run (with or without flouncing) she lets them run. When she doesn't it's clearly labelled a bad thing as with the huntee in BvsD or Riley's Vamp Ho in Into the Woods.