Needing BGO advice for a college student re-applicant

I am a re-applicant enrolled in an engineering program at my University. As advised by the USNA forum, I have selected classes that would closely approximate those of plebes: calculus, chemistry, engineering, writing, American History. I have done well in all my classes except chemistry where I stand a chance of getting below a C.
I can still withdraw from the course, but will have a W on my transcript. What would you advise?