She will not help the Lone Wanderer kill any super mutants, even if the Wanderer is being attacked. She will defend herself if attacked. She will cease-fire after the death of the super mutant that hit her, though, and other super mutants will not open fire on her.
Though Willow says that super mutants don't attack ghouls when ghoul wastelanders are spoken to in the random encounter "Ghoul-Friends," the ghouls will say "We were on our way to Underworld, but we couldn't get past the super mutants." This apparent contradiction is unresolved within the game.