It doesn't look bad to retake a class.
For AMCAS, a retake is averaged in as if it were any other new class. For AACOMAS (the DO application service) only the most recent grade is used to calculate the application GPA, as long as the credit hours are the same or better (though the old grade still appears). AACOMAS policy would allow for you to raise your GPAs rapidly. Some DO programs will consider you as you are if you've demonstrated recent strength in science classes.
Alternatively, if you have a recent string of good grades in the sciences, you might apply to get into an SMP (Special Masters Program) since your cGPA is >3.0 and you have a good MCAT score. Completing such a program with a >3.5 GPA can override your poor undergrad performance and make it possible for you to get into an MD med school. See the Postbaccalaureate Programs Forum for more information on this.
