I know a few people like this and can confirm: they're extremely difficult to be around and take pride in it, feeling great about being "free thinkers" and breaking from the "herd mentality".
This I feel is unfortunately counter to the design of humankind, where we are—as you said—social animals and the only way to change for the better—at a species level—is to change together.
Isn't that basis for criticism a little broad? It sounds like you're saying that vegetarianism, every religion, and a higher than average scrupulousness towards not littering are in the same category as picking your nose during a one on one.
I don't think so: those are strong convictions that people have according to their value system and moral code and it's their right to have them. I'm not talking about that at all. To me, those are "closed handed" issues: we respect them without negotiation.
I'm talking about "open handed" issues where people tend to debate and negotiate: preferences, not convictions—if 3/4 friends want to go get a sandwich, but 1/4 insists on either salad or "go without me", this can be taxing on the relationship—especially if they also are usually open to sandwiches and have no strong conviction against it.
People with strong value systems that differ from those around them are the freethinkers your friend with the tempestuous relationship with sandwiches is comparing themselves to.
It's not that people who clean up after camping have to drag all of humanity with them before they can claim to have done some good - it's that the sandwich shop example doesn't have anything to do with actual human values.
It's what they are, relative to a society that eats meat, doesn't really follow their self identified religion and that must put that garbage by the side of the trail somehow. :-)
This I feel is unfortunately counter to the design of humankind, where we are—as you said—social animals and the only way to change for the better—at a species level—is to change together.