Was his reaction plausible? In two words, Hell NO! They should be alarmed and shutting that facility down with the quickness. Only on television do we show diseases capable of completely liquefying human flesh and yawn.
I am not sure where the main character was supposed to have served but unless it was another planet, I cannot imagine where he would have seen ANY terrestrial disease which could have prepared him for what we witness in Helix.
Some of the world's most dangerous diseases can cause catastrophic damage to human flesh. Ebola hemorrhagic fever can liquify cellular tissue causing catastrophic damage. But only after a prolonged illness ending in organ failure and death. Another contender for sheer destructive capacity would be 'necrotizing fasciitis' also known as 'flesh-eating' bacteria.
The incubation period for Ebola HF ranges from 2 to 21 days. The onset of illness is abrupt and is characterized by fever, headache, joint and muscle aches, sore throat, and weakness, followed by diarrhea, vomiting, and stomach pain. A rash, red eyes, hiccups and internal and external bleeding may be seen in some patients. Mortality rates are generally very high, in the region of 80% – 90%, with the cause of death usually due to hypovolemic shock or organ failure. See: Ebola Virus Disease
But few terrestrial diseases should be able to prepare him for "black soup in a bag." This disease in Helix supposedly liquefies flesh, muscle and organs leaving only a tidy skeleton as remains.
Given the graphic nature of the damage caused by ebola or necrotizing fasciitism, I still can't imagine him being able to completely ignore the virulent effects of the disease on the skeleton and the attendant black goo which oozed from that body bag. Given the nature of some of the most dangerous diseases known to man, I would be hard pressed to find or name a disease whose characteristics were as potent or terrifying.
Granted, they are being portrayed as the most hard-core and knowledgeable disease technicians ever assembled but what came out of that bag should leave the most hardened disease specialists quivering in their boots.