There are many theories as to how the game of football (or soccer, as you Imperialist Yankee Bastards call it :D) evolved. The insitutionalised game we know as football these days seems to derive from early 19th century English rugby.
That doesn’t mean there are more ancestors to it. After all, the concept of kicking a round object around is universal enough to pop up in various corners of the world.
This means that there are many answers to the question “Where did soccer come from?”.
Here’s one that cites various origins.
It’s not unthinkable that an ancient society kicked the heads of their opponents around, and it’s not unthinkable that someone linked that with the game of football at one point or another. But I don’t think it’s a fair generalisation to say that soccer originated solely from kicking skulls around.