In the story wherein I wrote the werewolf killing the vampire, weres and vamps actually coexisted in harmony, along with mages and a few normal humans. This was just a special case of the vampire attacking and nearly killing the werewolf's normal-human boyfriend (while tripping out on mage blood, the vampire equivalent of LSD), driving the werewolf to kill the vamp in order to save her boyfriend's life. The vampire in question was a total nutcase. :/
I think it works whether it is a single instance or whether there is a war between the two. It is a fantasy world, after all. Vampires and werewolves aren't real; the only motivations they have are the ones you give them. So if there is a war between the two it is simple enough to provide a reason for it.
This sounds like an interesting scenario, though. The mage blood angle sounds fun.