Getting struck by lightning or having shipwrecks is not really a direct "murder" by the Valar. Its something that may happen naturally, without any interferance. And if the Valar decided "Hey, let's kill that person!" wouldn't they kill the king, and not random sailors?
Also, I think they wanted to give the Numenorians the last chance to repent. They wouldn't kill anyone; rather, they'd let the "misbehaving children" find their own end. (hey, that's just like Frodo with Saruman in the Shire!
)