Do you have an acceptance somewhere else? If so, then honesty will be the best solution here. If the school rescinds their offer, you still get to go to medical school. It may not be your first choice of school, but you can chalk it up to a lesson learned.
If you word it correctly, I think you could contact the school, and still have it help you. Something along the lines of this:
I am contacting you because I want to be sure everything I am doing is completely honest. Explain your situation here. . . The Certiphi background check did not reveal this infraction, and I am sure that the offense has been expunged from my record, but I respect this school and the privilege of practicing medicine too much to not be completely honest. I am willing to accept any consequence you deem necessary for this inadvertent oversight, and am hopeful that I will still be welcomed to matriculate in the fall.
So on and so forth. . .