User blog comment:EmrysOfAlbion/Emrys could have been smarter/@comment-4623180-20120503085135

The two answers below are right, imo, as he feels guilty for what she has become, and killing her may just make himself feel worse...

Also, maybe Morgana is powerful enough to endure the poppet. Plus, don't you have to stab it for the killing to actually take effect? I don't think he could risk walking in front of her and stabbing the poppet. (Not with Helios and the guards everywhere, plus Morgana probably has the power to defend herself when she knows it's going to be used on her) When Mary Collins did it, she was in the same room as the servant who was in there for a little while, maybe she was so easily killed because she was in the room for long enough for the poppet's magic to bind to her.

This I suppose is for us to decide- the producers have never said we can't make our own conclusions on things!

Here's for another interesting blog post. ;)