...that still wouldn't make the HH books non-canon. So, I really don't see it happening. However, there is already an in-game mechanic for the "HH books" to not exist: the fact that no one in the modern time period of the WH40K game (M41) knows exactly what happened. Most records were either destroyed by neglect, forgotten, or put under censure by the nascent Inquisition. Ergo, if you really wanted to, you can say that the HH books are all hearsay and rumors that only a fool would believe.
But, for those that care to *know*, the books give us concrete details.
http://www.lounge.belloflostsouls.net/showthread.php?52423-The-Blood-Pact-Chaos-Homebrew-Supplement&p=472214&viewfull=1#post472214
Got to be honest... Not entirely sure what the reasoning for this thread is but it compelled me to throw my tuppence worth in. Prior to reading a single Horus Heresy book, my knowledge of the background was that some geezer called Horus decided he could run the show better than another geezer called The Emperor (grandiose I know), in so doing the galaxy went a bit wonky and wound up with a bit of hair pulling and slaps until Horus was dead and The Emperor (grandiose I know) was put on the golden crapper for eternity. It didn't really figure much more than that and certainly didn't stop me enjoying getting LongFang spammed on an almost weekly occurrence. I am now ploughing through Fear to Tread, having read all of the preceding books and honestly having a whale of a time with it...
I remember my trepidation at the expansion books that hit and are still hitting the shelves for Star Wars, I resisted... And resisted some more.... Until I capitulated and read a friends copy of the Thrawn trilogy, from that point on I have bought pretty much every book, with the odd exception, Planet of Twilight; I have loved them all. Even when they decided to off Chewie... I was there cursing the Yuuzhan Vong...
I digress, I guess my point is nobody is forcing you to accept the background from the makers... So if you think the Emperor (grandiose I know) was a combover'd dirtbag, Horus was just a guy wanting his Papa Bear to take him the the football and buy him a hotdog and tell him he loved him or Lorgar as a jumped up dufus oh wait... You can. It's your hobby, likewise if you want to paint your Space Wolves' armour green, you can.
In summary, I think the Emperor (grandiose I know) is a jumped up, combover'd plank and my alien scum Eldar are anything but scum as they often host movie nights and charades with any race willing to get to their Craftworld. They also offer free parking and a valet service if you take out a loyalty card and attend atleast 3 outreach events promoting harmony and friendships per calendar year.
http://eldar-40k.blogspot.co.uk/