I'm not sure I agree. We're talking about a piece of merchandise, a product meant to satisfy consumers. Don't consumers have the right to give feedback about what they want in the products they buy? This isn't a free-speech issue, because the government isn't involved. It's an issue of commerce, of buyers making their preferences known to a seller. If, say, consumers petitioned a restaurant not to serve tuna that wasn't dolphin-safe, or petitioned a toy company not to make their toys in a country that used child labor, would you say that was over the line?
People have the freedom to express their views in public all they want. But if they want to sell a product -- which is what a work of professional fiction is -- then they're not guaranteed success, not in a capitalist system. Their work may get rejected by the publisher, or it may fail to get ordered in significant quantities by stores, or it may not sell many copies due to lack of promotion or bad reviews or any number of factors. In capitalism, you take your chances and failure is always an option.
Ultimately, of course, a petition is just a request, an expression of an opinion. It's still going to be up to DC to decide whether to publish the story or not. Just because a petition exists, that doesn't mean they'll obey its request. But the petition is a way for people to express their opinions to the publisher. It's audience feedback, nothing more. It's somewhat contradictory to say that Card has the right to express his views but the audience doesn't have the right to express theirs.