I am now reporting that on those 6 days I was hiking on the JMT and the extra couple I was hiking around Glen Aulin and May Lake, I did not use any filter or chemical treatment for any water I drank. I drank from many streams and rivulets, but not any muddy trickles across the trail
I drank directly from the Tuolumne River near Glen Aulin, from the lake outlet at May Lake, from many creeks and rivers during my trek from TM to Duck Lake, including the outlet of Duck.
I have been back in civilization now for 11 days and have shown no signs of any ill effects. I could have been just lucky, or the high water due to deep snow could have diluted the bugs enough that they could not infect me sufficiently for me to become ill.
I have been ignoring common knowledge and drinking water without treating it for several years now, and still believe we are being hoodwinked by the filter industry. I do not think that my own experienced eye is adequate to tell when treatment is wise or when it is not needed, but I do try to be a bit cautious. Water taken closer to the source has to be better than water closer to the ocean, right?
In June, I did just that. At the Oregon Hang, I drank from an Oregon river within 30 miles of the ocean, and no doubt a long way from its source. I did notice it was running high and clear, telling me that there was a good chance the dilution would protect me. I have no idea what crop or farm animals where upstream from that camp, but I am fairly certain there was no industry such as a paper mill or a sawmill.
This is just an anecdote saying we may not need to be so cautious out there.