It seems to me that true independant thinking in the Adam and Eve sense, is thinking that is apart from God. He being Creator of all things is also makes Him "the" determiner of Law/Limits/Standards/Systems. When we choose to live outside of His chosen parameters we become Lawless. To illustrate the deadly danger of lawlessness God has allowed the lawlessness of three individuals to grow relatively unchecked thru heaven and earth to become a near complete breakdown of orderly existence. Like cancer cells spreading though-out a body if left untreated the end result will be a complete system failure.
I think the fundamental problem is, we broadly generalize Independant Thinking into one negative catagory. We equate thinking independantly from God with Critical Thinking and thinking Independantly from others...which is not the case. One is healthy and good, one is not.