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 July.
In her ruling, Judge Garnett, a Biden appointee, 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”.
Garnett’s ruling was a setback for the justice department, which had called Thompson’s murder a “premeditated, cold-blooded assassination”.
The judge has given the government 30 days to challenge her decision to rule out the death penalty in the Mangione case.
In a win for prosecutors, Garnett said they could present evidence to the jury from Mangione’s backpack that he was wearing at the time of his arrest at a McDonald’s in Altoona, Pennsylvania.
Among the items in the bag were a gun, fake IDs and a notebook with writings that allegedly detailed Mangione’s grievances against the US healthcare system.
Defence attorneys had sought to dismiss that evidence from trial, arguing that authorities obtained it illegally without a warrant.
Mangione, an Ivy League graduate from a wealthy Maryland family, is also facing nine charges in a separate case brought by New York state prosecutors, including second-degree murder.
Garnett’s decision came as the defendant was due to appear in court for a hearing on Friday.
Father-of-two Thompson, 50, was shot from behind by a masked gunman as he walked to a midtown Manhattan hotel for UnitedHealth Group’s annual investor conference.
This week a Minnesota man allegedly impersonated an FBI agent in an attempt to free Mangione from the Brooklyn jail where he is being held.
The suspect – Mark Anderson – was carrying barbecue fork and pizza cutter, say prosecutors. He is now being held at the same facility as Mangione.