This is speculation. Based upon what we see in game. The Combine control everything. If its not to control the citizens of C17 then it was suppose to destroy them.
"Don't drink the water, they put something in it that makes you forget. I dont remember how I got here". - Civilian
The manhack arcade is also an example of this. Being that it is more active control and destruction of humanity then the death of a thousand cuts like the water, Air Exchange and Weather control.
Much like how the Air Exchange was used to keep people inside City 17 and control them by relying on the combine for air, water and food.. Weather Control was probably another way of doing that.
Remember in the original story-line there was "Acid rain"? The Air Exchange made the air toxic to breath while the rain made it toxic on your skin. Captain Vance had to target Weather Control because the conscripts cannot properly fight with gas masks on. Which also explains why the environments later in the beta are also not only dry but clear. No acid rain and no green gas.
Hope you liked this analysis.
-Manwich