The old Awakened Lands sourcebook indicated that in the outback many of the locals have a more benign view of the bugs as just one more aspect of nature. They also note that Termite hives are really the only refuge from mana storms. So you could have a symbiotic relationship between an outback town providing hosts (a la 'The Lottery') in exchange for a nearby storm sanctuary. Maybe the runners get hired by a disgruntled relative of somebody the town donated. Then when the runners start exterminating the local termites the local townfolk get to come to their defense. Or maybe while they're in town on other business a storm starts heading in and the townsfolk lead them to their friend's special fallout shelter... only to find themselves surrounded by oddly non-hostile bugs and not know what their long-term agenda was.

Another possible follow up on the factory vs town run:

After successfully putting the factory out of commission, permanently, the runners have to contend with the pissed off toxic shaman and his equally unhappy toxic spirit buddies. Maybe that's when the town's secret could come out (if the runners hadn't already put 2 and 2 together)?

If you really want to do a sympathetic Bug story, have the runners go on a mission to collect information from a top secret lab. They break in only to find that this lab is performing horrific experiments on Insect Spirits, so horrific that they make Josef Mengele look like a saint by comparison. They see hybrid merges in various states of mutilation and cyberimplantation, screaming in pain, begging for help. The team comes across a heavily-warded cell containing a beautiful young woman, just barely into her childbearing years, with no arms and only one leg, weeping. She does weep for herself, but for her children. She is a flesh form/good merge Queen. Having been mutilated horrifically to prevent escape attempts and metaphysically raped with high-powered mind control spells to force her to bring her children into this world of suffering for the profit of the megacorp and begs them for mercy for her children, to help her free them from their suffering.

And so the team has to rescue the innocent Invae from the horrible megacorp, assuming that they want to, while. Along the way they encounter cybered hybrid merges with Stirrup rigs and minigun arms being controlled by riggers in a secured bunker under the facility. And, of course, they have to carry around a low-force Queen who has no arms and who can't walk but who has some magical skills and who can keep the non-stirruped Invae from attacking the PCs.
During explorations they also come across the Big Babies, created by intentionally investing late-term pregnant women and by forcibly impregnating fertile female hybrid merges in an attempt to produce a metahuman with natural spirit powers.
If the runners shut down the facility the surviving Invae take their queen and the babies and try to find a place to make a home. Whether this is a good thing or a substantially worse thing that the experiments is merely a matter of perspective.

I think this is the point where most runners would say "OK" and shoot all the experimental subjects.


But it isn't just a choice between leaving the lab running and releasing the Invae. They can also kill everything, thermite the databanks, and do their best to collapse the building on the way out.