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After reading other people's thoughts on this, my best guess is that empowering Woedica is a mistake. Sure, Skaen promises that she will be grateful; but based on what we know about her, her notion of "gratitude" is probably along the lines of "I won't seek 'justice' against you for meddling in my plans, killing my favored servant and uncovering the secret truth bout the gods." She's just not the type to feel like she would owe you any more than that, because in her view, it is the duty of kith to serve the gods and not question; so everything you did in PoE 1 before you empowered her would be viewed as transgressions against her law that -you- owe -her- for. Empowering her means that you're even; nothing more.