it is in a separate disposable cup and an individual but piece of bread or a wafer...

I will not tear off bread from other peoples tears because of the fecal matter that is left on their hands, let alone other viruses that they spread including herpes.

The Point is to avoid making matters worse and this is an ideal scenario where tens, if not hundreds, COULD be infected.....and then the kids go to school on Monday.............

Steps need to be taken to ensure no cross contamination.

I am not a public health specialist. But I would think that it depends on how Communion is offered. If it is offered by handing out little pieces of bread and having wine/grape juice poured into separate unreused cups, I would assume that the chances of catching the disease would be smaller than if offered by allowing sips from a common cup.
I would guess that the method of dipping the bread into the cup might be fairly safe.
Of course, swine flu can be caught by other methods as well, such as having an infected person sneeze on you without covering his or her mouth.