Lots of doctors operate their businesses as sole proprietors, and not all firms that employ doctors provide malpractice. (Granted, that's a shitty policy, but it happens, and it's even a bit theoretically justified since it might cut down on moral hazard.)
Sole proprietors still have business expenses that are separate from their income, which comes after. Additionally, anyone making Doctor money who runs their business as a sole proprietorship is a fool for not protecting their personal assets from their business dealings.
Even if all the physicians were to decide to do their accounting the way you recommend, one would still need to make adjustments for the costs of doing business, when considering reporting of income like that found in TFA, which certainly does not include such adjustments.
It's not a matter of "decide to do their accounting." Business expenses are business expenses, even if you're a sole proprietor. It is a business expense, therefore it comes before your salary. Just like any other business expense, you could technically not choose to claim that business expense, but then you'd be paying income tax on that money. But you could also choose not to claim your office space rent, the salaries you pay your administrative staff, etc. Those things are all in the same category.
Private practices would indeed have their expenses arranged in the fashion you describe, i.e. with those qualifying expenditures counted as business expenses before pass-through. The caveat is that titling the private practice as the malpractice policy holder, so that the insurance costs become business expenses, exposes the corporation to lability, not just the individual physician. For practices involving multiple physicians, or which own/rent property to operate a clinic, this liability exposure can be undesired. Relating from a relative who is a physician, who has been a contractor and an employee, I have to stress the general point that professional expense accounting for doctors is quite unique, due to substantial involvement of insurance and regulatory concerns. It's not easily relatable to other professions. Likewise, doctors, despite making very generous compensation, are often still frequently struggling with their employers/contractees, or with 3rd parties like insurance providers, pushing costs onto them. Since telemedicine doesn't really exist in significant form, doctors don't always have the option of quitting and finding better work in the same city/state.