Synchrophasors are timestamped data from individual measuring devices on the power grid, such as relays. If you can control those devices on a live system you absolutely can do a lot of damage. However, there are often several layers between those devices and the phasor data concentrator. And more security between the PDC and the public internet.
Synchrophasors' value is in comparing voltages across entire synchronous regions[1] to maintain stability and prevent events like the 2003 Northeast blackout. As such, they're essentially national in scale. How do you get information across the country (in roughly real time) without the internet? As you can imagine, replicating huge chunks of the internet is cost prohibitive to even the largest utilities.
Believe me, networking is taken extremely seriously in my industry (electric power), and no device is connected to the internet unless it absolutely has to be. There are plenty of valid concerns; however, progress must still be made. I'm interested to see how this all plays out, and to play my own small part in the development of networked utility infrastructure.
So far, the power grid has been safe from the types of nuisance attacks the water utility in the article saw. I really don't know why water pumps and sanitation systems need to be online. I have a hunch we electrical engineers have a leg up on civil engineers when it comes to computer security. ;)
[1]https://en.wikipedia.org/wiki/Wide_area_synchronous_grid