Was [SPOILER] Murdered In Real Life?
Christopher Nolan's films are told from deliberately subjective points of view. This is especially true for "Oppenheimer," which presents scenes and events differently depending on if they're being remembered by the man himself or by his greatest adversary, Lewis Strauss (Robert Downey Jr.). When the audience is shown the two different versions of Jean's death, they're depicted as flashes of possibilities tormenting the guilty J. Robert Oppenheimer.
It's telling that the first conclusion he jumps to after hearing the news is that she may have been murdered, regardless of whether or not it's actually true. Admittedly, Oppenheimer had been given cause for this concern by Leslie Groves (Matt Damon), who warned him about what the violently anti-Communist Colonel Boris Pash (Casey Affleck) might do to his associates. Perhaps it's possible, in the continuity of this film at least, that without Oppenheimer revealing to Pash the name of the potential Communist mole, the Colonel made a grimly justifiable leap in logic and went to interrogate Oppenheimer's most well-known Communist associate. That's what Oppenheimer seems to imagine at first, anyway, arguably to distance himself from guilt as much as possible.
It's only after he sees Jean taking her own life in his mind's eye that he tearfully accepts responsibility for her death. While he may be doing so in the case of either scenario, it's possible the flashback implies Oppenheimer's acceptance of the truth. Whatever tragedy befell Jean in real life, the ambiguity is almost certainly meant to be a window into Oppenheimer's guilty conscience rather than mere historical skepticism.