i stand by my opinion that teh procedure was unnecessary....... if the do that to check for viruses, it is obvious that they are going to find them because you baby has kennel cough, rendering the process unecessary and from what youre post also said (potentially more hazardous to youre baby becuase he started to get REALLY sick after they did it)
IMO i wouldnt let those vet (or teh vet techs) play off of you, i would go and tell them what is what