I agree that zero tolerance is a bad idea, but what they've struck down is the "reasonable person" standard in any kind of criminal case. It has nothing to do with zero tolerance.
IANAL, but I suspect the issue is that to convict someone for a serious crime you generally have to show "mens rea" ("guilty mind") -- that the defendant had the intent of committing the crime in question. If so the ruling may be reasonable, but not for the reasons you suggest. If I'm right, what SCOTUS is saying is that the jury has to determine that the husband actually intended to threaten his wife.
As for the civil liberties implications, they appear to be more limited than most people seem to believe. Threatening someone is still a crime. It's just not a crime to say something someone would misconstrue as a threat, even if that person is being reasonable.