I don't know of many situations in which the players just stumble on a dragon lair, and the dragon tells them to leave it alone because it hasn't done anything. And yes, if the players then decided to kill it anyways, it would be an evil act.
First, how many of the dragons that V just killed do you suppose fall into that category?
And second, I'll again remind you that the OotS invaded the lair of the first black dragon and killed it to get the piece of starmetal they needed to reforge Roy's sword. They were not out to stop an evil, rampaging monster - they just wanted to acquire a magic item to increase their power. Back when that strip ran, I don't remember anyone claiming that the OotS had just committed an evil act.