Alike and equal are not the same, because people should have equal rights without being forced to be like everyone else.
On Camazotz, conformity is the rule. The kids should all bounce the ball the same way. Anyone who does not do things exactly like everyone else is re-educated. The populace is controlled by fear.
When Meg is trying to prevent herself from being brainwashed by IT, she tries reciting nursery rhymes, and when that doesn't work, the “Declaration of Independence.” The concept of people being equal appeals to IT, and Meg ends up arguing with IT about the difference between “equal” and “alike.”
"But that's exactly what we have on Camazotz. Complete equality. Everybody exactly alike."
For a moment her brain reeled with confusion. Then came a moment of blazing truth. "No!" she cried triumphantly. "Like and equal are not the same thing at all!" (Ch. 9)
If people have equal rights, that means they can make their own choices. On Camazotz, people have no rights at all. If they do not want to do things like everyone else, they are out of luck. You can have different concepts that are equal, but still different. For example, if someone wanted to bounce a ball on the ground, and someone else wanted to bounce it off a wall, both of these are equally good ways to use a ball. They are not the same.
The concept of uniqueness is an important one in this book. Before her journey, Meg was frustrated because she felt that she did not fit in. As she went along, she came to see how her unique skills and personality traits made her special. On Camazotz, being strong-willed and independent saved her from IT. Charles Wallace was not so lucky. He was more easily taken in by the seductive nature of IT's message.