Better Education Before the Enlightenment?

When public education was first started, students learned scriptures, the curriculum was based on Biblical beliefs, and churches ran most universities. Harvard University even originally started out as a training facility for future pastors and ministers. 

In today's society however, the only schools that are even allowed to mention scripture publicly are the private schools. Public schools are too vulnerable for being sued and suffering other reciprocations for even mentioning God in class. The government in California is even going as far as to say how parents can educate their children. Lawmakers in California have discussed making homeschooling illegal and have discussed the option of shutting down private schools as well. If this were to happen, no parents would have any say as to how their children would be educated. Their children would be forced to go to a public school where the theory of evolution and other such topics are discussed and taught.

After the enlightenment, people began having new ideas. They felt they should have the ability to educate themselves. Many also felt they could learn everything they needed to through their senses. Society got away from the idea of having the church educate them, to the idea of educating themselves or by learning through nature and other resources. 

This brings me to my question: knowing how drastically education has changed as a result from the enlightenment (going from being Biblically based to being 100% against Christianity), was the enlightenment really a good thing? Even though we are now able to make many necessary decisions for ourselves, was it worth taking God out of our schools?