I agree that failing OChem twice looks bad, but I'm sure you have a good story to tell about that (or will come up with one) for an essay about "Challenges overcome". Besides getting the A, you can further redeem the bad impression you've left by acing OChem II and/or Biochem on the first try, as well as some upper-level Bio.
Schools won't average three efforts to pass a class, thus negating the 4.0 eventually earned (it would take too much work on their part, anyway). The intent of stating a minimum grade is so you have a guideline for retaking classes you didn't sufficiently master.
The point where one would be screened out automatically (via computer-driven cutoffs) would be the overall BCPM GPA or cGPA. This gives one a chance to washout the negative effect of some bad grades with a sea of A grades. Stats-wise, what would make you ineligible for MD schools would be failing to demonstrate a steep consistent upward grade trend, having GPAs below those cutpoints (typically 3.0 for less-selective institutions, but some schools go lower), and not having a strong enough MCAT score to compensate and prove you "got it" so that adcomms are reassured you will thrive in their program.
In WAMC you'll read about folks who got a second bachelors degree, eventually ending up with 200+ undergrad credits, in order to redeem a poor academic record. Others go the SMP (Special Masters Program) route if they have the cash. Or you can apply to AACOMAS DO schools which have a grade forgiveness policy and save time and money.