A limitation on the earlier (43-1) study is not
necessarily a limitation on the later case-control study. The authors
of the bibliography are quite correct when they state that a
case-control study could measure a net protective effect of firearms.

Dr. Paul H. Blackman writes:

The earlier study noted that one couldn’t fully evaluate the protective
value of firearms without knowing about their use in non-fatal
protective situations. I.e., the authors recognized that a gun could
be used for protection without producing a corpse.
The later study did not note that one needed such complete knowledge in
order to evaluate the protective uses of firearms.

Because the methodology was different. The case-control method can
measure net protection from homicides. For example, if all the
respondents in Kleck’s DGU survey spoke the truth, then over 500,000
homicides are averted each year using guns. If we make the (perhaps
unrealistic) assumption that guns can magically prevent all
household members from homicide, we would expect to see zero homicides
in the half of households with guns, and over 500,000 each year in the
gun-less households. Kellermann would have found no gun owners amongst
his case subjects and ended with an odds ratio of 0.00 — indicating a
very very strong protective benefit. If, instead of being magic
talismans, guns only prevented half the potential homicides in
gun-owning households then there would be 500,000 homicides in
gun-owning households and 1,000,000 in the gun-less households.
A case-control study would find that 33% of the cases owned guns and
50% of the controls owned guns, giving an odds ratio of 0.50 —
indicating a very strong protective benefit.

A case-control
study which measures only deaths cannot measure a net protective effect
of firearms.

Yes it can — see above.

You are simply mistaken. You can only be correct if a
gun has no protective value shy of producing a corpse,

Nope, if a gun prevents someone from becoming a corpse, that benefit
can be measured.

and if the only
crime from which one wishes to be protected is a homicide.

It only measures protection against homicide, not against other
crimes. A protective benefit against homicide is ipso facto a
protective benefit.