I'd like to point a possible flaw in your counter-argument: jQuery wasn't the only choice and it wasn't the first. PrototypeJS, which came before it, did an arguably better job since it didn't have many of jQuery's design flaws, like hijacking 'this' or silent selector errors.
The PHP analogy is therefore spot on IMHO: both it and jQuery (and I'd like to throw MySQL in there while we're at it) were tools that achieved success by lowering the quality bar in exchange for feature abundance and "if it works why do you care how".
I overlooked the fact that PrototypeJS was first (in fact, I was one of the unfortunates who backed that horse), but I still disagree. I don't think the jQuery lowered any kind of quality bar, it made absurd and redundant work irrelevant.
If you're referring to those legions of people who "don't know javascript, but know jQuery," without jQuery they simply would have been lousy javascript developers instead of lousy javascript developers, that doesn't change anything.
You bring up prototype of all things as an argument for having less design flaws than jquery...sorry, I really don't want to sound snarky, but that made me chuckle.
Their moronic choice of directly extending the DOM was a more fundamental and far-reaching flaw than any of the - definitly numerous - problems and bad choices jquery has and had in the past, and it's one of the reasons it's has all but vanished for years now.
The PHP analogy is therefore spot on IMHO: both it and jQuery (and I'd like to throw MySQL in there while we're at it) were tools that achieved success by lowering the quality bar in exchange for feature abundance and "if it works why do you care how".