I don't think you'll be penalized for having incomplete prereqs. The physics on the MCAT is relatively light (if disguised as quite complicated by the stem). There is, however, guaranteed to be some form of physics II concept tested like light, optics, magnetism, etc.
My concern for you has more to do with your attitude regarding math and exam taking. Math, especially the simple algebraic manipulation required for physics, is not going away. You'll see some (admittedly, very basic) algebra in biochem and physio as an MS1. You'll certainly have lots and lots of exams ahead of you. My recommendation would be to get comfortable with your algebra skills. Lose the conception of yourself as someone who is "bad at math." You're learning math, you're practicing, you're getting better. Make a google doc and every time you make a mistake, log it in your google doc and you'll soon have some data that may show some trends. For me, it is often simple arithmetic mistakes that trip me up. Do practice problems. Do the ones that are hard that you hate. Do them again if you get them wrong and don't instantly look up the answer!
Regarding exams, it sounds like you have some anxiety issues. Speak to a school counselor about this, exam anxiety is a real phenomenon and it can be fixed. Imagine the anxiety from a 7 hour, career-deciding exam like the MCAT. Tackle this before you get to the MCAT and before you reach medical school and you will be so much better off!
FWIW, I also considered myself "bad at math." I failed precalculus! I struggled through physics and Chem II due to my fear and anxiety around my past experiences with math. When I realized that my self-image as "quantitatively challenged" was impacting my performance and started to alter it, my scores got better. When I challenged myself with regular practice, my grades improved further. Good luck to you!!!