I really recommend reading the thread at http://coris.noaa.gov/exchanges/coralfuture/coral_future.pdf - this is a discussion by working scientists, and although it's from 2001, the predictions of the demise of coral reefs were already very current then. It's a good introduction to the huge complexity of reasoning about these systems, which involve more feedback loops than a non-expert can even imagine. What I take away from that discussion is that there is no serious researcher in the field who doesn't see the coral reefs disappearing at a huge rate, but there is no consensus about the dominant mechanism; I think (although I am not an expert) that the arguments of those who see pollution and overfishing as the main cause are more persuasive.

For example, a very large fraction of coral reefs around Sri Lanka disappeared in the 1990s, and this apparently had more to do with the fact that people blasted them and hauled them away to be used as limestone in the construction industry, than with any subtle changes in the pH of seawater. In the (very plausible) opinion of some of the scientists from that discussion, most coral reefs will die off long before the pH changes really become significant. It would be great if someone who is a researcher in this field could give us some more recent results and data.