Even the prosecution seemed to say that the initial reaction was justified because the other guy was aggressive and hostile in a crowded train, but that the measures taken to subdue him went too far

From the New Yorker article linked in the posted article:

“His initial intent was even laudable, to protect fellow subway riders from a man he perceived to be a threat.” But the law does not permit “laudable behavior” when it is also “unnecessarily reckless,” Yoran went on. Her opening statement—in which she described how Penny held Neely in a choke hold for almost six minutes, even after the train doors had opened and the other straphangers had fled to safety—concluded, “The defendant was not justified in these deadly actions. He used far too much force for far too long. He went way too far.” Later, the jury—twelve jurors and four alternates, all hailing from Manhattan—would need to decide for themselves whether the Assistant District Attorney was correct.