It's not has if it would be built at Ground Zero. Because of what happened, I highly doubt anything will be built there for a very long time, if ever. It's a place for those who lost loved ones to mourn and visit as well as a place to honor the hero's and victims. Nothing will change that.
I don't think a Mosque being built in New York is a bad thing. I'm sure there are Mosque's all over the state. We are still the united States, after all. Freedom of Religion is one of our amendments. Just because someone is connected to the culture doesn't mean they are all Terrorists.
And I could be wrong, but aren't terrorists religious extremists and not necessarily affiliated with a particular religion?
Either way, I don't see it as a bad thing.