How well warranted is this assumption, i.e. that a typical reader takes the quality of MoR for granted?
A typical reader of this post, mind you.
Readers of LW who don't like MoR will probably have a strong tendency not to be interested in "rationalist fanfiction" in general. If someone reads LW and is also willing to entertain a rewriting of a famous fantasy story such that the characters are made to be LW-style "rationalists", it seems highly unlikely that they're going to be turned off specifically by the idiosyncratic details of MoR.
Given this, I think the assumption is very well warranted. Of course, it's eminently falsifiable: if there are large numbers of people who love the idea of rationalist fanfiction but hate MoR specifically, let them speak up.
I am not interested in MoR not because of its idiosyncrasies, but because I have no interest in Harry Potter, have read none of it, and the characters are completely alien to me. I am neither a fan of Tolkien, but still find it more appealing, and at least I know one person who likes LotR and has poor opinion about HP. Also, sometimes I read posts whose topic isn't particularly interesting, because sometimes inspiring ideas appear in the discussion.
Generalising from one example I had impression that readers of this post may not all like MoR.
This may be old news to some people, especially the Russian speakers, but I didn't see an article about it here.
In 1999, Kirill Yeskov, a Russian paleontologist, wrote The Last Ringbearer, a 270-page take on Lord of the Rings from the point of view of a medic in Mordor's dying armies who is also a "skeptic and a rationalist." In fact, Mordor represents the forces of reason in this retelling of the story. As a Nazgúl (himself a former mathematician) explains, Mordor is "the little oasis of Reason in which your light-minded civilization had so comfortably nestled." Barad-dur is "that amazing city of alchemists and poets, mechanics and astronomers, philosophers and physicians, the heart of the only civilization in Middle-earth to bet on rational knowledge and bravely pitch its barely adolescent technology against ancient magic."
The story has been newly translated and is available in free PDF form -- in English and the original Russian. There's a recent review from Salon as well.