The difference is that Sylvanas knew the souls of the Kaldorei would go to the Maw. Elune presumed the souls of the Kaldorei would go to Ardenweald, and thus granted them a painless death in slumber to ease the terror and agony of burning alive. It was Elune’s intention that those souls would go to her sister and ease Ardenweald’s difficulties.
Had Elune known that all souls were going to the Maw, she’d have acted differently. Sylvanas, by contrast, knew all souls were going to the Maw, and acted intentionally.