Seems you verified what I suspected NJO sucks
So i think the solution is clear - say the NJO era didn't exist, that would give Disney and Lucasfilm the perfect playground to work with. And their actions would not affect the previous good stuff that you mentioned alone. And seeing as support for the NJO era is minimal, they can get away with pretending it doesn't exist and carving out their own chunk of space to work in. Not sure about the whole timeline thing, but this may lead to the death of the whole Darth Caedus/Lumiya arc - I don't know.
Slippery slope, 3 will become 52+ before you can say Yuuzhan Vong...
At a push i could except an alternate NJO era - but labeled as non-canon (like starwars infinities) Thus in a canon-sense that era could be erased and the films accompanied by fresh EU can take its place.