Perhaps in the future all entryways will operate via automatic door. Or bathrooms will be totally non-touch, like at some airports (“maze” doorway instead of a door that needs to open for each visitor, no-touch urinal, no-touch sink and soap dispenser, motion activated hand dryer).
Recent studies suggest that pet exposure, particularly in early childhood, may have beneficial effects and may actually prevent the development of atopic disorders.
Altho not definitive, it is suggestive that living among a large amount of germs may be beneficial, overall. The problem the OP is after, tho, is a conundrum - how to be more selective of what we are killing (target COVID and not everything else).
Unfortunately, that’s a real estate question, more than architecture. I’ve been in plenty of San Francisco restaurant restrooms that are smaller than a maze entrance. One in particular that I can think of has about four square feet of floor between the toilet and the door so there’s just barely enough space to walk in, do your business, flush, and turn around to leave. The sink is next to the room.
Contact-free restrooms have been gaining traction in airports and some stores over the past couple of years, at least, so it is a good trend.
As for the hygiene hypothesis, I’ve been a Renaissance Faire participant for quite a while, and we joke about how dirt is a seasoning, and that we all have very well-exercised immune systems, so I’m a believer.