I've found it's easy enough to ignore canon - you just have to establish early on that that's the way you're going.
One of the conceits of much of the published Realms (particularly Ed Greenwood's work) is that it comes from an unreliable narrator. The Realms that we know is the the Realms as related to Ed Greenwood by Elminster (why is probably why Elminster is so awesome and gets laid, like, all the time). Heck, the Volo's guides all come with a foreword warning the reader that Volothamp is full of crap.
My suggestion would be to embrace that. Establish early on in the campaign that Elminster is, in fact, a Marco Polo-esque hack who big notes himself through stories and claims credit for other people's actions but is really a middling wizard who isn't even the first to use the name. The Seven Sisters are the offspring of of some fey lord who seduced their mother (who was later killed by their father in a jealous rage) -- the whole "children of Mystra" thing is just a legend that they didn't deny because it was useful. Essentially every thing the players might think they know about the realms could be a lie, the product of stories that may or may not be true.
The reason I like this approach is that it keeps canon useful without being bound by it. It aligns player knowledge with character knowledge - published canon is the "truth" of the realms as understood by the characters, but the actual truth might be quite different.