Was it a good idea to leave Charles Wallace on Camazotz?

The answer to this is complex, because Meg's father is forced to choose between two of his children. Meg is in danger of IT taking control of her mind, but Charles Wallace has already been taken control of. Therefore, Meg's father has to make a quick decision about what is best for the safety of all involved. In this case, that decision is to tesser to another planet with Calvin and Meg while leaving Charles Wallace behind, even though he is still under the control of IT on Camazotz.
Ultimately, however, this does prove to be a worthwhile decision. While it is dangerous to do what he does, leaving when they have the chance gives Meg the opportunity to learn more about the tesseract, about the universe, and about the concept of love, with which she is ultimately able to free Charles Wallace from the control of IT. Perhaps it might not seem to be a good decision at the time, and Meg is certainly upset at her father because of the decision that he makes, but in the end, it is in the best interest of all involved.

It was not a good idea to leave Charles Wallace on Camazotz, as he was left in the grip of the evil force that had taken control of his mind. However, Calvin, Meg, and Meg's father had little choice but to escape when they did. IT was taking control of Meg's mind too, as she was unable to resist its strength. The only way to wrest Meg from IT was to tesser out to another planet.
Although it was not ideal to leave Charles Wallace behind, it was better to save Meg and come back for Charles Wallace then to leave both of them in the grip of an evil power. Meg, at first, couldn't understand this and was angry at her father for not managing to save both his children at once.