The analogy itself is dicta: part of the decision’s explanation and commentary; not a statement of law or binding precedent. Therefore not something that can be overturned in the subsequent case.
AFAIK the courts did not find this. After all, they were not considering the case of someone who shouted ‘fire!’ in a crowded theatre. If someone actually did this and people died as a result (e.g. in a stampede), it seems highly unlikely that a free speech defense could be used.
I get your point, it's just a bad example given the historical baggage.