I think the way they animated it in the anime was very good... not to gory and actually pretty brutal if you consider at what time this show is aired..
I don't need them to show me limbs getting cut of like in Elfen Lied :/
the "gore" when Haku was killed by Chidori was cool enough... sure thing, I wouldn't mind seing it with a bit less "lightning effects" because they really blurred the picture a bit.
but then on the other hand, it wasn't a problem to see that Kakashi's hand is really IN Haku's body.. especially when he grabbed his hand and Kakashi tried to pull it out of him.
personally I wouldn't call chidori an assassination technique in the first place, even though they said it is one... they say that the victim can't make out where the sound is comming from etc. but for me, an assassination shouldn't make a noise in the first place. especially if you target is someone who is waiting in his room which is heavily guarded.It's the first time I've seen how the manga does it, and you can really see, rather than told, that Raikiri is an assassination technique.