well born women would almost certainly be much more intelligent than someone from the poorer classes
Not really. Better educated, yes. But really it'd be the opposite, retract difficult conditions for a few generations and you have a higher chance of the stupider genes slipping in, while a poor person with those genes might well be dead and thus unable to breed. Perhaps along with Yatwer, another textual flag in regard to the poor.
But that Esme happened to turn up just in the right place and time? Remember Kellhus actually loves her - the neural activity for that love is hidden away amongst everything, while K declares himself be beyond human or whatever. He's working in arc, rather than shortest lines.
Also the world conspires. Or in the end, the authors been showing his hand, quite explicitly, all along. It's the way we can keep looking past that authorial hand which is part of the lesson.
Also he had a bunch of ill fated concubines as well, because hey, when your the boss, just do whatchu wanna! Who's to say they weren't all carefully chosen for intelligence? Thus Esme being his wife doesn't really matter anyway, in regards to efficiency.