I think the question of whether or not killing Snowman makes the end natural is one to ponder. Who is to say that her death causes an unnatural end to the universe? Keep in mind that the troll's universe is undoubtedly much older than ours. After all, we know that they have had movies for long enough that all the creative titles have been used. They've achieved a much higher class of civilization than ours, considering that they have achieved space travel, and possibly FTL travel (though I find it more likely that they are merely able to travel at an extremely high percentage of c.) This indicates that a great deal more time has passed since the beginnings of their species than the beginning of ours, and thus a great deal more time for their planet, and, progressing logically, their universe. Perhaps (metaphorically speaking) their Bilious Slick decided to have kids extremely late in life.
Beyond that, I find Scratch to be a rather... unreliable narrator. He claims that he doesn't lie, but then he does so in a baldfaced manner, before clarifying that it was for the sake of a joke. (Also, he's just kinda an asshole and I don't like him.) I believe he also says that if the revelation of the lie is delayed for long enough, it becomes a prank, which he does extremely rarely. Granted, I can't imagine how "My master is an evil man" could be made into a joke, except maybe in the cosmic sense.
Besides, from Scratch's point of view, LE could be considered evil. After all, Scratch himself must die to summon him, which undoubtedly causes some resentment. He goes along with it because of inevitability, but he's had centuries, maybe even longer, to stew upon that resentment.
Anyway, that's my theory.