Jury selection in the federal trial is scheduled to begin on 8 September with opening statements due to start on 13 October.
But state prosecutors are seeking to try Mangione as soon as 1 July.
In her ruling, Judge Garnett said two of the four federal charges did not “meet the federal statutory definition of a ‘crime of violence’ as matter of law”.
She noted that her decision was “solely to foreclose the death penalty as an available punishment to be considered by the jury” ultimately responsible for Mangione’s verdict.
Garnett also said prosecutors would be allowed to feature evidence from Mangione’s seized backpack that he was wearing at the time of his arrest.
Among the items in the backpack were a gun, fake IDs, and a notebook with writings that detailed Mangione’s private healthcare system grievances.
Defence attorneys had sought to dismiss that evidence from trial, arguing that authorities obtained it in an illegal search.
Mangione is also facing nine charges in a separate case brought by New York state prosecutors, including second-degree murder.