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In Overlord II the alignment isn't of the same type of Overlord and Raising Hell where you can choose between "good" and "evil", but between the "Domination" and "Destruction" paths, which are both considered to be two sides of the same evil. Essentially the game presents you with a question: you want to rule the world or to destroy the world? As you can see, there isn't a "good" option, just two types of evil.
About the Fay question, if you want to pursue the "domination" playstyle you must choose the "Dark Fay" option. When the time will come in which she will appear in her new form of "Dark Fay" you'll have to just wait for her to enter in the closer portal and resist to the waves of elf warriors. Just wait half a minute. If you want to pursue the "destruction" playstyle you must kill her with magic in her "Dark Fay" version while she is attempting to reach that same portal, and so obtain the "Ghost fay" version.
Other tips I can give about the domination playstyle is: don't kill 1000 gnomes, or you will gain Destruction points; when you use the Evil Presence spell against a target release it just till you see an electric violet halo on its head or it will die; use Evil Presence spell to enslave all the inhabitants of the conquered towns and their leaders, don't kill them (this does not apply to unprovoked hostile inhabitants, you can safely kill them).