I think Eric Freeman gets this right:
If forced to bet, I would assume that the arena will eventually be built at the Pier 30-32 site, if only because the team continues to get better (and therefore more popular among casual fans) and vast amounts of money tend to help in citywide votes (the results of Measure B notwithstanding). Yet it's also likely that arguments over the Warriors' plans will get more heated, largely because the underlying issues aren't going away any time soon. The project faces opposition not just because of its specifics. Ultimately, the question up for consideration is how much an organization that represents the Bay Area to the basketball-loving world cares about understanding and continuing to promote the historical character of the region.
What's left out, though, is that San Francisco, while quickly transforming into a rich-person's playground, is also the one major American city that has consistently rejected public financing for big-time sports palaces.
The San Francisco Giants nearly moved away in the 1970s and 1990s because voters in and outside the city rejected stadium funding, only to be kept in the city when Peter Magowan spearheaded an effort to built a new downtown ballpark with minimal public funding. And the San Francisco 49ers will move south and out of town, starting next year, because voters rejected spending city money on a new stadium and mall at Candlestick Park's location.
That's how I see the current conflict: Yes, it's about whether the team recognizes the historical character of the region, but tied up in that is a recognition that, historically, San Francisco doesn't pay for arenas.
(Image cc-licensed: "Golden State Warriors vs. Portland Trail Blazers" by Antonio Fucito)