Some of the local stores seem to turn over their stocks very quickly. Under those circumstances, I think really sick fish don't have sufficient time to develop symptoms so they appear to look healthy. Aside from the usual parasitic suspects, I think pathogens can decimate a system with little recourse, especially if its viral.
Marc, I suspect some of your coral issues are indirectly related to your fish problem. It sounds like the less tolerant SPS varieties have been the first to go which is probably due to the diminished water quality as the fish die.
I think the course of action you are going with is probably the best. Get the fish out and let things stabilize. I have a 100g rubbermaid tub you are welcome to use.