Using an enchanted item to kill violates the First Law (this is supported in the books,
there is a scene near the beginning of Summer Knight where Dresden avoids flattening two hitmen with his ring
).
The Warden Sword doesn't violate the First Law because it is a sword (it is "mundanely" able to kill by virtue of being a sharp piece of solid metal). There isn't a beam of magic light shooting from the sword to the target.
As to why the sword cutting through spells doesn't violate the first law is because ending a spell usually doesn't lead to inevitable death. I am having trouble coming up with a non-contrived example.
If a fugitive practitioner is standing on a "force bridge" of magic that spans a 200 foot drop, I suppose counterspelling it would be a violation of the First Law.
But if a fugitive is cowering behind a barrier, cutting through the barrier just ends the barrier, it doesn't kill the fugitive (like blowing someone off a cliff would do). It just leaves the fugitive vulnerable as anyone else would be.
The option to use Warden Swords as Weapon:6 by using a charge (see the update to Enchanted Items) does seem a little strange, but they are supposed to be REALLY sharp.