Has society become too germ adverse that it is becoming unhealthy?

Yes, I think so. There are certain places you want to be germ free like an operating theatre or a food production line, but otherwise a bit of dirt don’t hurt.

Leaving behind 0.01% of the bacteria is not good because the ones that survive are resistant to the anti-bacterial agent and no longer have any other bacteria competing with them for food. Best to forget the anti-bacterial sprays and use normal detergent and water for most things. If you need something germ free, you want to kill 100%, using either bleach or heat.