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I don't want Emma to kill anyone either.  |
No one wants Emma to kill anyone, but she will certainly do something very dark next season, or there would be no point in making her the D.O..
IMO, making her the D.O. might be (operative word MIGHT) the show's way of getting her to do something she wouldn't ordinarely do, and then explay "it wasn't really her, but the darkness inside her pushed her to do it".
For to even make sense for them to go after Merlin, Emma has to be in some danger of being influenced by the darkness.