It is important to note that it only counts as killing with magic if the intent of the spell directly is to cause death. For example casting a spell that makes your sword burn? Not killing with magic. Casting a spell to cause a boulder to fall and that boulder kills a person? Not killing with magic.
Casting a spell to deliberately cause a boulder to fall and kill someone with magic is. It's a fine line though and many wardens will be likely to kill you for the grey area but intent is important.
Particularly with enchanting, you can enchant a weapon to do lots of nifty things that make it deadly as long as it isn't enchanted to kill. Shapeshifters are another good example, if you shapeshift into an animal and kill them you are killing them with magic sure, but the magic's purpose was to change your form, not focused on killing. The books talk more about this distinction I believe.