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I'm going to disagree with everyone and suggest you take the C (but push really hard for that B without groveling).
Are you planning on applying this cycle? That might affect things. Even if not, what are the chances you'll be able to take the class with a different professor next (or another) semester? If you end up with him/her again, would the W and possible C (again) be worth it? Going through the same agony again, except semester-long? Your sGPA will take a hit now, no doubt, but if you're ORM, it's medium for MD as is. You're fine for DO. Even with the C, you'll be fine for DO. If you're URM, the C will have negligible to zero effect.
I have not taken OChem II, but I had a similar situation with OChem I two semesters ago. I really thought I was heading towards a D. I ended with a B with my incredibly grade deflating instructor at the local CC. I am glad I stuck it out and got the B - I would not want to repeat that semester with 6-hr labs on Fridays and all the disruptions to my work schedule. I got a B, but I would have been OK with a C on that course just because of the time drain it was and the fact that I would only be able to take it again with the same grade-deflating professor. No point.
Sorry to toss this contrary note into this pool of unanimous opinions.
Edit: my thread - To Drop or Not to Drop?
3.4 GPA (before another C) is not average for MD for ORM. Your rationale for OP to stick it out is that he should feel like he doesn't want to do the work all over again? I would want the best chance at medical school I could grind through even if it meant adding a year to my app, but whatever floats your boat.
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