According to Richard Dawkins - evolutionary biologist, atheist, writer, science communicator - the whole notion of nature in harmony which your post presupposes is an illusion. He describes the situation we're in and I mean all life by "we" as one of "selfish cooperation" and I have my doubts whether he intended his words to be taken seriously. The tone of his writing suggested an attempt at ironic humor.

Who knows. I doubt it's as directed, insidious, or "intelligent" as some may infer from your premise. Though, it is an interesting concept. Since we began to become "cleanly" or embrace "cleanliness", we unnaturally remove the germs and microbes that have been on our bodies for, allegedly, millions of years prior. Perhaps this assumption is but a conspiracy theory. Perhaps not. However, in the years leading up to the Black Death that wiped out half of Europe (1000-1200 A.D.) this did occur.

Bathing is [has become] essential to the Western European upper class. — Human history

Of course. Who knows.

Edit: I infer or imply the possibility of germs, viruses, or microbes building intrinsically natural immunity from unnatural and man-made stimuli, as documented here.

Doe combination of increasing population, the squeezing of other species out of their living space, and reliance on complex technology result in evolutionary instability that is favourable to the creation of deadlier viruses? — Jacob-B

While this requires qualification, I say no, no, and no to the three points above. We should say that despite the increased knowledge and modern technology, there will always be micro systems of diseases (viruses) that will co-exist with all the other systems we have in place. We are the transmission mode of these contagions -- our bodies are the perfect host and carrier. Unless we become androids or some sort of beings that aren't biological, we are in perpetual vulnerability.

The black death in the 1300s came at a time when modern inventions and technology were (it can be argued) 'comparable' to our time. And there's not a billion people back then.