With the recent purchase of the Star Wars franchise by Disney, the old canon has questionable bearing. Previously, the canon structure had the films (G-canon) above the EU novels (C-canon). The key point to note is that the EU was still considered canonical, but Lucas was not beholden to it (i.e. he could invalidate it with new films or TV shows if he so desired).
Under Disney, the old EU works are no longer considered canon, being rebranded "Legends", but new works (those starting with A New Dawn) will be on an equal footing with the films. Post-ROTJ works are explicitly non canon for now, though they may choose to incorporate elements of them in new works. It is rumored that older (pre-Ep III) works will be incorporated into the new canon, as Disney's focus is primarily on the post-ROTJ timeline, but this is as of now unconfirmed.
So in answer to your last question: Yes, as of now, all post-ROTJ EU works are non-canonical.
With regards to your first question, no, I have never seen any attempt at reconciliation towards that in the EU. One of the central themes of Star Wars has been the struggle between good and evil, and the balance of the two, which in EU works obviously continued long after the fall of the Empire. Lucas has on several occasions made statements and then contradicted himself, so such a broad statement must be taken with a grain of salt. Lucas' own view of canonicity was more restrictive than the guidelines set forward by his company, so you have to choose how much to follow one set of guidelines or another.
In regards to relating the Chosen One to balancing the force in the EU, see either of the top two answers (disclaimer: one of them is mine) to this question, and note that the accepted answer does reference that same quote, though not really in the way you were asking.
