Life finds a way. I think in some ways, CCD has probably "pruned" the bee population in a good way. Beekeeping allowed weaker hives that would have normally died off in the wild to continue to spawn new hives. CCD has reversed that trend, and may have improved the overall strength of the bee population genetics.
You are right and wrong. It's true that introduction of new diseases and parasites were a part of what is called CCD, and to the extent that hives with genetic strategies both of immunity and behavior were the survivors in the usual evolutionary way, then the remaining stock should be more robust (although of course that isn't necessarily "weaker" hives, and who knows what kinds of genetic variation was lost due to a lack of a particular success strategy against varroa for example). However, CCD is rightfully attributed to pesticides, fungicides, and a host of other human created stress factors on bees. Colonies survive these collateral stresses for the most part by luck, and not by any generic advantage. You are right that beekeepers have artificially extended generations of bees whose natural defenses might have failed against new parasites and diseases (that we ourselves imported into their populations), and that some die off was inevitable as result of natural balance being reached, but I'd say there is a good argument to be made that CCD interfered with this process rather than aiding it.