"According to Bunker, the average person gains about 5.25 years due to medicine"
and then calculates "year of life the doctor saved" based on that. That's wrong.
The counterexample: the kid breaks the leg. The leg will "heal" even without the operation, but the form will be altered: the kid will never be able to walk normally, do the sport normally, anything you imagine (a). A few operations are performed on the kid's leg, afterwards he walks normally, lives the rest of his life normally (b). Now if the person having the problems in (a) lives the same number of years as the fully healthy (b) the statistics the whole article calculation is based don't show any contribution of the given operations, whereas these operations really did "save life" in the sense of giving somebody a healthy life that he otherwise wouldn't have.
There are immense number of equivalent examples and all are ignored in the article. Much more lives are effectively "saved" by the modern medicine than the author can see. We can also consider the lives of the family of the patient also effectively "destroyed" without the medicine.
(In short, the article appeared as (stereotypically said, more as the strong figure of speech not actually addressed at the specific author) written by 20-something male who hasn't first-hand experienced medical problems even in his family. I wasn't able to find more about "Gregory Lewis" who wrote it, but the whole "80,000 Hours" project site, on which this 2012 article was published was the result of the 2011 initiative of two Oxford students, and maybe that gives some idea about the setting.)