Aside from the inclusive fitness claim, Cochran's gay germ hypothesis is also consistent with the continued existence of homosexuality: the pathogen co-evolves and so while the genes do get selected against, which genes keeps changing. Unfortunately, his theory still remains something of a 'germ of the gaps' theory - no one's come up with a remotely plausible theory or found decent evidence that homosexuality spikes the fertility of relatives so much as to compensate for the sterility of homosexuals (remember, inclusive fitness decreases fast: if a homosexual has 1.05 rather than 2.1 children, then their siblings have to have 2.1 additional children, their cousins 4.2 additional children, and so on), so a theory which merely isn't contradicted by any evidence looks pretty good by comparison.

One thing I thought of which would be direct evidence for the infection theory: polygenic scores for homosexuality. It's somewhat heritable, so given a large sample size like UK Biobank, it should be possible to explain a few % of variance and construct a PGS based on a fairly narrow age cohort like 1 or 2 decades. Then the PGS can be applied longitudinally outside the sample. If it's pathogenic co-evolution and the relevant genes keep changing, then the homosexuality PGS should show highest predictive validity in the original age bracket, but then decrease steadily as one moves away from the age bracket into the past or toward the present, showing a clear inverted V shape. While polygenic scores can increase or decrease steadily or show sudden shocks for various reasons just like heritabilities can increase/decrease over time (eg education PGS decrease due to dysgenics, height PGS increase and so on), they don't typically show a distinct V shape, so finding one for homosexuality would be very striking.