People absolutely need to determine how serious or dark their game is going to be ran.
I think having the 'default' lean towards 'there are no evil cultures' in a setting which often leans into High Fantasy (Good vs Evil) tropes, makes very little sense.
I think retconning Lolth dominated culture would be a mistake, as I dont believe you need to remove these elements from the game at all. Lolth is a villain. The party is (often) Good. Good adventurers stand against villains, and if you play with dungeon delving, kicking in doors, and multiple encounters a day to expend your abilities, well you need "Bad Guys" to do that against.
If you wish for your world to run as a 'mostly peaceful world where adventurers just explore and meet other people to talk to' I mean, fine, I certainly hope you enjoy that game.
I think it's a move from "high fantasy assumptions" to "Superhero genre assumptions" (everyone is good, except a supervillain like Thanos, totally unconnected, with unbelievable ideas that you can see are wrong, but who has the individual power to cause great harm, unless the heroes, of equal power, can move against him).
Can I interest you int my campaign instead, where the heroes boldly defeat the Archpriestess of Lolth and her plan to delay the international agreement to progressively phase out a 2% export tax on non-ferrous alloy until reasonable compensations are granted? We'll have a BLAST.Its not FR though at that point, by a long shot, so play it in Eberron or some other world.
To be honest, that's not my Eberron either. I play it, as KB puts it, as a world on the brink of collapse barring heroic intervention. Everyone is selfish, avaricious, self-concerned, xenophobic, bigoted, well, humans (as in real-world, not the fantasy race known for its lack of darkvision) and they need to be saved ; it's just the question of choosing who the bad guy will be for the campaign at hand: dragonmarked houses (think Arasaka on steroids), the five nations (minus one of course), the Blood of Vol, the Aurum (even the setting's Reform Club can be a den of villainy), the Lords or Dust (who want to unmake the world) or the Dragon, (who oppose the Lords of Dust but have no qualm if ensure it means removing all gnomes from the prophecy)... It's certainly more gritty than intended but I think it makes room from providing... lifelike villains.