I'd definitely say that Nocenti's original version- of Typhoid as life-long victim of mental trauma- is the one that should be canon. Aside from being the creator's vision, it was a constant theme in so many of Typhoid's storylines that dispensing with it for a rather random tie-in to Miller's Daredevil run seems very silly. (And I loved Kelly's Deadpool, don't get me wrong). If one really had to keep that part of her history for some reason, I'd retcon it by saying that was a time when the Typhoid personality was dominant, but that Daredevil kicking her out the window somehow caused a resurgence of her psychosis and brought Mary back into conflict or something. Probably best to ignore it, though, as I think that it is reductive and it really diminishes the tragedy of Typhoid's character and the impact of so many of her stories that deal with mental trauma.