As you noted, but for the record and for emphasis, Markup's discussion of headline tags includes the statement "Please note that <h1> and <h2>are discouraged here.</i>."

Failure to honor that guidance does NOT, IMO, amount to a case in which "someone misbehaved again...." where my understanding of the connotations of this usage of "misbehaved" include "deliberately flouted the rules." I suspect this is more like the case of the AM or noob who ignores the guidance re para tags posted (even more prominently) at our text-entry box.

As to the merits of disabling <h1>, 2 & 3 -- my $0.02 worth is that even if use were regarded as a mortal sin, felonious mis-formatting, or some other semi-egregious violation of the Monastery's generally accepted conventions.

Take a node that's been posted in ALL-CAPS as a parallel (a sorta' weak onethough because (IME) the whole internet community pretty much subscribes to the notion that doing so is rude ('shouting!'). That happens here at least as often as the use of the larger headline tags but we probably can't cure the problem by disabling upper-case letters... and its probably not worth the trouble to build a filter that will correctly revise an all-caps node.

And finally, you've already mentioned what seems a reasonable solution: let those who chose use CSS to specify rendering a headline tags at less-than-pure-html size but add no needless complications for pmdevs nor any new Monastic mysteries for those who don't share your objection to the current rendering, or who (were we to adopt the option of site-wide css modification of h1 and h2 tags) wouldn't understand why theirs came out so small.