Yes, but the lede is why. They don't really get to anything resembling a resolution until something like 1/2 to 2/3 of the way through the article. Even now I'm still unsure whether the 500k excess deaths were rabies infections or due to tainted water. They never got around to providing much clarity on that front. The paper only goes so far as to say a) more rabies vaccines were sold, b) people saw more dogs, c) fecal counts in water went up, and d) DO in water went down. But that comes with two huge caveats:

Feral dog data were collected after the ban and "do not allow us to reject that feral dog populations were already higher in the high-vulture suitability districts even before the collapse of vulture populations."
Fecal coliform also has human origins. And the uptick in fecal counts (along with the decline in DO) was in areas where more people live.

Correlation between excess human deaths and vulture decline wasn't actually teased out into any kind of causation, and the best they could do was link death upticks with spatially isolated poisoning nodes. Urban areas had a more pronounced effect, but urban areas have a lot of other factors that can cause death, and none of those factors were controlled for, or really even mentioned in section 6.2 or the conclusion. Overall the paper is crappy because the study is quite poor, so I guess the author did the best they could with a study that tried to do far too much with far too little data.