This is my self-serving answer because I really, really like horror towns and want some new ones to visit... but wanting to keep your cute town is understandable. My town is a cute town too. (I'm not skilled enough at pixel art to make a horror town of my own, sadly...)
Why not make a cute horror town? Keep the town cute but have an area of sparse dead trees and make the houses pretty cute but have something sinister in them like a well used axe, or just make a creepy as all get out basement.
Why do you want to create a horror town? Depending on your reasons, you could include the things you'd want in your cute town or get a second copy of the game.
I like the idea of mixing the two like people have suggested! You could use pink,purple,black, and white flowers! Like black, pink and purple roses, white violets! And have dead trees scattered around. OR make a section far off in a corner that suddenly all the flowers go black and there are things buried and skeletons and dead trees. (I have a section like that surrounding my witches hut) Or just get a second copy ;p