Superior Court Judge Robert Perry also dismissed part of a conspiracy count against Stern and Dr. Sandeep Kapoor, ruling there was insufficient proof that the two men conspired to obtain controlled drugs through fraud and deceit.
Perry allowed the balance of that conspiracy charge to stand and ruled the bulk of the 11-count complaint would go to the jury for a decision.
Stern, Kapoor and Dr. Khristine Eroshevich have pleaded not guilty to conspiring to prescribe, administer and dispense a controlled substance to an addict. They are not charged in Smith's 2007 overdose death.
Perry has been critical of the prosecution case and previously said some charges would likely be dismissed. But he noted Tuesday, "there is a presumption (in the law) in favor of letting cases go to the jury."
The legal arguments have taken up so much time that closing arguments have been delayed until Monday.