I agree that demolition for the sake of demolition is a waste. But demolition to make way for new development is something different, and can be a good thing. There are plenty of cases (particularly in other cities) of positive new developments. One in Jacksonville, I'd argue, is the current Main Library.
In the case of the Shipyards, they didn't just tear it all down for the hell of it, it was going to be a new development. That just didn't happen. But even still, it's not as if they tore down the buildings and just left it there. The developers did a considerable amount of work cleaning up the environmental contamination and bulkheading the property, to the tune of over $30 million, IIRC. That's money any developer would have had to spend, whether adapting the old buildings or adding something new.
At any rate I think that's the bigger issue in Jacksonville - allowing demolitions to make way for new developments that are never completed, or for projects that don't make adequate use of the space (like parking lots).