Here's a possible litmus test: how would you feel about another former Orthodox Jew desecrating a Torah scroll as a symbol of eir change in belief.

"Another"? I assume this question is directed at Joshua Z. I am not a former Orthodox Jew, nor any other kind of Jew for that matter. I'm Catholic.

That said, as I wrote in my above comment, clearly the context of an offensive/blasphemous act or utterance matters a lot. As for the concrete scenario you list, I find it hard to imagine that a Jew who has left the religion would symbolically desecrate Torah -- the act has such a strong connotation of anti-Jewish pogroms that I'd imagine even a non-religious Jew would find it scary, almost like brandishing swastikas. That's my outsider's impression at least; I'd be curious to hear the opinion of someone more knowledgeable.