Disruption and contamination is a constant concern in an ecosystem ecological research, particularly microbial work. I think of it as being somewhat akin to the Heisenberg uncertainty principle, the more deeply you investigate an ecological system, the more likely you are to mess up the that system.
That being said, these folks are professionals, I guarantee you that the first thing they did was collect the microbial samples. Further, there are sterilization protocols in place to limit contamination:
http://www.nature.com/news/lakes-under-the-ice-antarctica-s-secret-garden-1.15729
From the article:
"Although contamination is always a concern, researchers not connected with the Lake Whillans project say that the sterilization precautions seem to have worked well. One sign is that the microbial density of the drilling water in the hole was 200 times lower than that of the lake samples, says Peter Doran, an Earth scientist at the University of Illinois in Chicago, who worked with the US National Research Council for ten years to develop guidelines for sampling Antarctic lakes cleanly. Doran was convinced by the evidence of diverse microbial life in the lake. “They found it in such a way that it can't be questioned. It's pretty iron-clad,” he says."