The figure of 60,000 fatalities due to malaria seems ridiculously high.
The figures published by the Medical Departments of the various United States armed services in the years after the war provide a figure in the hundreds, rather than in the tens of thousands.
- US Army - 302 deaths due to malaria between 1942 and 1945
- US Navy & US Marine Corps - 87 deaths due to malaria between 1942 and 1945
I haven't been able to locate figures for fatalities due to malaria in the U.S. Army Air Forces (USAAF) (which may be included with those for the US Army above, or which may have been reported separately under the auspices the US Air Force after the war) and US Coast Guard between 1942 and 1945, but it seems highly unlikely that those would bring the total anywhere near that quoted in the article you cited.
Chapter XVII of The Medical Department of the United States Army in World War II, Vol II Infectious Diseases (available on Google Play) deals with the treatment of malaria during the war. The figures presented in the text are much lower, suggesting a total number of fatalities in the hundreds, rather than the tens of thousands.
The Defense Technical Information Center publication Internal Medicine in World War II. Volume 2. Infectious Diseases states that there were 302 deaths of US Army personnel due to malaria in the period 1942-45, 10 of which were within the United States (p460).
Table 61 in the text presents a breakdown of that total, and is reproduced below:
US Navy / US Marine Corps
Volume 3 of The History of the Medical Department of the United States Navy in World War II contains a detailed breakdown of the Statistics of Diseases and Injuries for the United States Navy and US Marine Corps.
Appendix table 1 contains a breakdown of "noncombat injuries" (which includes those suffering from various diseases, including malaria). According to that table (the relevant section of which is reproduced below), there were only 87 fatalities due to malaria between 1942 and 1945, although there were almost 90,000 cases treated:
(The fatalities are listed in the column "DD" ("Discharged dead") under "Dispositions during the period".)
For completeness, the meanings of the abbreviations used in the table are explained on page 5 of that volume as follows:
A (new admission), which denotes that the patient was taken up on the sick list from a duty status with a diagnosis which was not causally related to any diagnosis for which previously admitted or was a separate, distinct, and new occurrence of a previous disability.
EPTE (existed prior to entry), which signifies that the patient was taken up under the same circumstances as described for "A" but that the diagnosed condition was considered to have existed in the patient prior to his entry into the naval service.
ACD (admitted contributory disability), denoting- a disability considered to be a complication or sequela of another diagnosis for which the patient had been previously admitted to the sick list.
AD (additional diagnosis), which indicates an additional concurrent or intercurrent disability in a patient who is on the sick list because of some other disability
D (duty) which indicates that the patient was returned to duty.
DD (died), which signifies that the patient died.
IS (invalided from the service), which denotes that the patient was invalided from the service upon the approved recommendation of a board of medical survey or was placed on the retired list because of physical disability.
"Other,'' which includes those patients whose diagnosis was changed and who were continued on the sick list under another diagnosis, those still on the sick list at the end of the period, and those who deserted while on the sick list.
That figure of 87 fatalities agrees quite closely with the PubMed article you quoted, while the total number of new admissions (113,744) is very close to the figure of 113,256 in that article.
This would suggest that the anti-malarial drugs employed by the US military during the Second World War were very effective when they able to be administered.