Agreed, I don't think there are any specific penalties other than loss of fiduciary protection. Which means the risk is from a participant lawsuit, which is generally not going to be worthwhile.
Your experience may be different, but among prospective clients I've met with recently who have "1099 workers" about half really have misclassified common law employees. If the clinic has common law employees, the answers to your questions will be different.
Re the form of transaction, of course there would be a deed for the portion of the parcel being sold that would go to the buyer and a new deed showing remaining portion owned by plan. Consult a real estate lawyer or perehaps title company.