does any of the water used, then become unusable and leave the water cycle? of course not... water use is not the problem, water contamination is... runoff from farms and ranches both is a part of that problem..
I was going to mention this, but ya beat me to it.
One interesting facet of this topic that I've been studying is the use of so-called "Gray-water" as irrigation. Pretty much eliminating the need for sewer systems outside of dense population centers.
If one were to build a semi-subterranean home into the side of say, a hill, it would be no difficult task to divert gray water downhill to your garden/farm. Of course, we would have to take into consideration what is allowed to get into our waste water to begin with, but there are health benefits involved with eliminating the use of things that might contaminate said water, making it unsuitable for agriculture anyways. Win win sort of situation, ya know?