The only real argument you could make is that the govt wanted to see what happens with the virus after X years in an isolated environment, but thats kind of stupid. There is zero ability for any bacteria or virus to survive 80s industrial/military incinerators so it doesn't really make any sense they did it for safety.
I just thought it was funny none of the other team members seemed to react, like all they saw was the dude fall down and then elizabeth fire a gun. Sure, maybe he got infected or maybe Liz and Phillip were told to execute the team after extraction.
I know it was artistic and all to have a 6 minute pit digging sequence but it was pretty easy to guess ahead of time what they were doing ("he has to do one last service") so I thought the whole thing was a bit too much. Still a great episode, I especially liked that dinner scene where Elizabeth is clearly angry at someone for criticizing the USSR and Philip clearly is thinking that maybe capitalism is better.
Also interesting how much corruption was talked about in the episode, usually we think the USSR fell because of inefficiencies (the farming scene) and inability to keep up technically but corruption was such a huge part of it, and sort of makes you wonder how corrupt the top countries are nowadays.