There is a News and Views article "Mesoamerica's Mystery Killer
" in Science about this disease. It is not a peer-reviewed scientific paper, but a news article. The main hypothesis according to the article is that heat and dehydration in combination with other factors are responsible. But it does mention the pesticide hypothesis and the researchers asked about it were rather skeptical:
He points to research from Sri Lanka suggesting that glyphosate in
pesticides chelates arsenic, boosting its level in the water and its
potential to damage the kidneys' delicate filtering machinery. And his
team has preliminary evidence that arsenic levels are higher in fields
surrounding the cemetery than in the nearby village.
Wesseling, who has built her career around studying the impact of
toxic substances, says his arguments have no merit. She says neither
pesticides nor arsenic can explain the geography of the disease.
Arsenic, she says, is prevalent in soil and lakes across El Salvador,
not just where CKDu is common. "It doesn't convince me at all," she
says. "He's only looked at one specific place."
Cruz of Hospital Nacional Rosales agrees. "We need other hypotheses,"
The general idea presented in that paper is that glyphosate is able to chelate metals, which is well-known and not controversial. The distribution of the disease is correlated with water hardness according to the paper, so they speculate that a metal-glyphosate complex is responsible for the disease. They speculate further that the metal-glyphosate complexes are not metabolized in the liver and then released in the kidney.
The article behind this theory is explicitly marked as "hypothesis" in the journal, and it does not actually contain any data. The only actual new data related to the hypothesis it mentions is a study currently conducted in California. This data is pretty much impossible to interpret now as it is only roughly described in the article and does not mention any control group or any further detail.
There isn't really anything to debunk here as there is no evidence in the first place. The entire article is speculative.