Spoilers
IT is still alive at the end, just too weak to regain control over the protagonist without the protagonist giving IT back that control by choice. IT got so powerful from 'consuming' all the victims you set free at the end of the game. It'll take a while before IT gets that powerful again.
The reason why you can go back at the end is a bit more technical. I REALLY struggled with the choice to allow it because it meant letting people replay the game and see things they might've missed.
I was really considering making it impossible to do so by removing the LOAD option in the menu and having it be that you only see the empty box for a few seconds whenever you press the start the button - a way of respecting the protagonist's struggle and final decision to move on.
I also considered letting people replay the game at the cost of losing all their progress and having to start over from the beginning, but I landed on what you experienced as the final result.