"It’s very disturbing, and sort of a backstory for what It is, or where Pennywise came from. That might be something worth exploring in the second one. The idea is the ‘It’ entity was dormant for thousands and thousands of years. The [flashback] scene hints on that."
So what exactly happened in this scene that made it so disturbing? Reddit found the answer, in the form of the script, which contained the scene. Spoiler: if you had a hard time handling watching Pennywise devour a young boy, you're not going to enjoy hearing what he does to a much, much younger child.
The scene is set in 1637. A woman named Abigail rushes into a well house clutching her baby. She slams the door, as if the devil is after them. Suddenly, a small candle chandelier above her begins to spin.
"[It] shape shifts again. A beam of light passes, revealing PENNYWISE, naked, lithe, flesh pale and translucent, a half- formed imitation of a human, opens his maw full of large razor sharp teeth, dripping with saliva... Each time the light hits his face, It’s different. A Man. A Woman. A Beast. A Monster."
Then again, there will eventually be a sequel to this movie. Plenty of time to put the scene back into the film, and maybe even enough time for us to mentally prepare ourselves for seeing it. In the meantime, if you like being scared by creepy clowns, there are plenty of real life options for you.