The meanings are different.
1. You are taking her with you, aren't you?"
It means, "I expect you to"; "I want you to".
2. You are taking her with you, are you?
Two possible meanings:
a. You are just repeating what the other person has told you, just to make polite conversation. Example: "My husband is a lawyer." " Your husband is a lawyer, is he?" This technique is used by politicians and royalty when they meet people at a garden party or on a walkabout.
b. It means, "Oh, is that what you are going to do? I didn't know that."