@Tomislav - I may not be able to spell it (I always want to spell it as coxsackie virus or even coxsakie), but I can pronounce it. However, you may just want to visit Cocksackie, New York to find out just how it is pronounced as it was named after the town of Cocksackie.
But as far as the dictionary is concerned it is pronounced, just as you suspected, just how it looks "cock-sack-ee".
The interesting thing about it being typically a tropical weather virus, is that it is named after Cocksackie, New York because the town did have a small outbreak and a nearby laboratory made the discovery.
But I agree, at a school with medically fragile students this virus is one you want to know about.