More often than not I find the show's 'conscience' when it comes to whose death is a just one is more or less arbitrary and based on the main characters and who we're supposed to like, more than anything else.
For SERIOUS. It is Bad and Wrong to kill Uther even though he has killed lots and lots of people, but the rest of time Arthur and Merlin will quite happily kill their opponents and enemies rather than defeating them in other ways, and these enemies usually deserve death because they're killed (or attempted to kill) people along the way.
And with Nimueh, she doesn't even do that! Merlin asks her to do something, accepts the consequences, and when it doesn't go to plan he offers to sacrifice himself instead, but when Gaius gets there first he ... decides Nimueh must die. I have no idea why. It's very Uther 2.0, as it sounds like it's pretty much exactly that series of events that got magic driven out of Camelot in the first place, and it's not exactly Nimueh's fault!
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For SERIOUS. It is Bad and Wrong to kill Uther even though he has killed lots and lots of people, but the rest of time Arthur and Merlin will quite happily kill their opponents and enemies rather than defeating them in other ways, and these enemies usually deserve death because they're killed (or attempted to kill) people along the way.
And with Nimueh, she doesn't even do that! Merlin asks her to do something, accepts the consequences, and when it doesn't go to plan he offers to sacrifice himself instead, but when Gaius gets there first he ... decides Nimueh must die. I have no idea why. It's very Uther 2.0, as it sounds like it's pretty much exactly that series of events that got magic driven out of Camelot in the first place, and it's not exactly Nimueh's fault!