Let me see if I get this straight -
If it happened on screen, it should be honoured? That's relatively straight forward.
It's the next bit I'm confused about - If Gene Roddenbery wrote about it, but it didn't appear on screen it still happened or is real and should be honoured? is that right?
Please somebody explain it to me.
I'm not sure if you're kidding or not, but here goes with an attempt.
My take on it is that since JJ has absolutely violated both the visual appearance of things and the historical happenings we know were established ON SCREEN (which has been, up to this point, absolute canon), then this new movie has broken away from the existing STAR TREK universe, and has become a something else. a "nu" STAR TREK universe or "reality".
Of course, we'll have to wait and see exactly what reasons are given for Kirk's entire crew being under Pike's command and the red/blue/gold uniforms being in place when the Enterprise passes from Kirk to Pike (since WNMHGB) shows none of that to have been the case.
There's also the very look of the Enterprise itself, inside and out.
If the ship's looking different and the crew/uniform thing are somehow a result of the Romulans messing with history prior to Kirk getting aboard Pike's ship, then we might be able to say this is "sort of" the same universe, but forever altered...at least for now. (Maybe as time passes, things will "iron out" and much of what came later will still be in place.)
In either case, prior "canon" has been trashed by this movie. We can't be sure of ANYTHING from this point on, and will have to accept the fact that STAR TREK is actually starting all over again. (And as said above, maybe as of TNG things might be back on track, but for Kirk's era, the canon change has been made.)