Hi,
The population under study included 32,000 Northern Malawians. Mortality measurements were taken from August 2002, before the availability of free ART, to February 2006, eight months after the opening of a free ART clinic. The clinic opening serves as an exogenous shock to the system - independent of other factors that might affect changes in mortality rates - and thus serves as a type of natural or quasi-experiment from which reliable impact estimates can be gathered.
The system? which system? political system? health care system?
The phrase 'a shock to the system' is idiomatic, usually meaning simply 'a big shock'. eg Here is an example from a blog at http://www.newleaftheatre.org/blog/category/new-leaf-community/
It’s always a shock to the system when you live through the same events as someone else and as you look back, they somehow have a completely different experience than your own.
It's hard to know what exactly is meant in your extract. The author could be thinking of the health care system, or of the whole social system within which these people live. I think the general idea is just that the introduction of the new clinic made a big change to everything, "shook everything up".
Best wishes, Clive