Currently, there is a bug in which Illia is no longer recruitable after you send her home. When you talk to her, she will respond with generic dialogue (much like a guard), and you are unable to choose any speech options. A solution on the PC to this is to open the console with the ` key, select Illia, and type 'setrelationshiprank player 1'.
If you change into a werewolf form during the quest, Illia won't attack you, neither in the tower nor in the final battle. If you use the Fear cry, she will be affected, but won't retaliate. She can also start a conversation with you, but you can't start one with her.
If you have Illia as a companion and trade with her, you can receive a closet key which can be used at a key-only door in the Darklight Tower. Inside the closet is a group of potions on a cupboard.