SKR is a fine writer, and more FR produts by him would be welcome.
However...it's silly to think that the Realms are going off the rails just because you don't like a free web product.
Complaints based on recent FR products would be more meaningful. But the Spider Queen adventure seems to have been well-received, and I, at least, think Races of Faerun is great, too.
WotC is moving the Realms towards more player-oriented products. That's no secret. Magic of Faerun apparently greatly outsold Lords of Darkness. Even the regional books are moving in that direction --- Unapproachable East will have far more crunch than Silver Marches, and there may be a FR Player's Guide on the way.
Personally, I like this. I like the products so far. I like that more people are exploring the Realms. I like that WotC will continue to produce FR products.
As has already been pointed out, time travel has always had it place in the Realms. Putting that aside, this one little article hardly signifies a major shift, does it? I suppose anything on the WotC website is "canon", but as with any element of a RPG world, you aren't being forced to integrate it into your campaign.
Since this time portal isn't in print form, I'd wager that you can just ignore it, confident that it is extremely unlikely that any future FR product will even make reference to its existance.