Clean and unclean

Clean and unclean - was being unclean considered a sin? Or merely a temporary state that required rectification? Yahshua (Jesus) did things that rendered himself unclean when it was necessary to help someone or to make a point. Did this just show that being willing to be made unclean was acceptable when the situation demanded it? What was the result? Anyone unclean was not allowed to serve in the temple until they were clean again. From a health standpoint, that makes good sense, i hope people now with contagious diseases or something unhealthy stay away from public meetings.

I've thought that the whole deal with YHWH requiring the Israelites to use running water and standards of cleanliness was a way to protect 'primitive' people with no understanding of germs. But when was it noticed that contagion existed? And the earliest civilizations had indoor plumbing - do we just assume this was merely for convenience? Or did they know more than we think?