I think you're most likely right, but it's still interesting in terms of panspermia. These have to be some pretty sturdy bugs to survive at that height - the oxygen concentration at 41 km is 0.3% of what it is at sea level. Also, IIRC, the ozone layer is mostly concentrated between 15 and 30 km, so they have to be getting some pretty hefty doses of UV radiation. If you can survive at 41 km up, you're not far away from being able to survive in space itself....
I believe that is already confirmed. I will find the link if you wish.
An important point that is NOT addressed in the article is the reason for suspecting that the microbes are other than terrestial in origin: the convection layer of the Earth's atmosphere doesn't extend to 40km. IOW, there aren't many other viable mechanism for transporting large volumes of microbial material from the earth's surface to these altitudes.
Really big volcanic eruptions could probably do it, as would really big meteorite impacts, but both are fairly rare events.
Beyond that, I'm hard pressed to see how the buggers get up there (unless someone can show that Brownian motion is sufficient to propel microbes to an altitude of 40km (about 125,000 feet.) Hitch-hiking on rockets and stratospheric research ballons is about the only other imaginable sources, neither of which would ever get any significant volume of microbes up there.