The planet is not Lavos's body. Let us assume for a moment that the planet is a living organism itself ala FF7, or better yet, that the planet is the Entity. That makes Lavos a parasite living inside the planet, and, as with symbiotic relationships between different species, what's bad for the host is bad for everything that lives on the host. This makes Lavos evil from the planet's point of view. And, whether or not one considers the planet and Entity the same, from the Entity's point of view it seems Lavos is evil as well. My point is, the majority of creatures and beings consider Lavos evil. Not just from humans' point of view.
And scratching one's skin is not needless destruction of creatures. Considering the size of the planet, I'd say an earthquake equates to the planet scratching an itch. While there is death of organisms in an earthquake, it's not intentional.
Lavos bursts out of the ground, which can not be considered his body, and 'Rains fire down from the heavens!' That is intentional destruction, not scratching an itch.
And, unless for some strange reason you don't consider the original 2300 AD to be a dead or dying planet, then Lavos is indeed a sentient, evil parasite.