If only the men are killed because women are considered useful, is that really so different from men being killed simply for being men?
As for the whole whether "Kill all <historically persecuted/minority group>" should be considered equivalent to "Kill all men", I suppose one way to justify treating them differently is the likelihood of anyone actually taking such a suggestion seriously. We know there's been at least one massive-scale attempt to kill (virtually) all Jews, and we know there are still people around today who admire the ideology behind that and could potentially develop the capability to carry out such an attempt - I don't think, despite the list of examples just given, you could seriously suggest there's a group of people with sufficient admiration of an ideology that says "all men should die" and a capability to attempt carrying it out.
As for the whole whether "Kill all <historically persecuted/minority group>" should be considered equivalent to "Kill all men", I suppose one way to justify treating them differently is the likelihood of anyone actually taking such a suggestion seriously. We know there's been at least one massive-scale attempt to kill (virtually) all Jews, and we know there are still people around today who admire the ideology behind that and could potentially develop the capability to carry out such an attempt - I don't think, despite the list of examples just given, you could seriously suggest there's a group of people with sufficient admiration of an ideology that says "all men should die" and a capability to attempt carrying it out.