I suspect when they inevitably revisit that period that it'll be massively simplified and a lot closer to what Lucas envisioned: One Jedi preaching a greater embrace of the Dark Side is expelled but takes a whole chunk of the order with him. He later looses control and is killed and all hell breaks loose across the galaxy. The Republic falls, the constantly splintering Sith Empires rule the galaxy until they eventually all but destroy themselves.
No Sith species, no galaxy wide wars that are over in five minutes because the Jedi commit mass-genocide. I could see certain characters and events being re-purposed into a new context, but by and large I think it'd be a lot different from what we've seen before.
Personally what I'd lake to see is the Jedi before they became what they were in the Prequels. I have a general notion that the Sith schism was a wound the Order never really recovered from and the Sith Wars were really the beginning of the end for the Jedi. The last millennium after Bane was just a slow decent into stagnation.
I wouldn't go so far as to call it "head canon" exactly, but I do have a general notion of what I think would make a more interesting trajectory for the Jedi than the one presented in the old EU comics.
Firstly, that the Jedi at their peak weren't a weird, religious order of Space Police, but an entire galaxy spanning civilisation of force wielders in a time before the Mortis Gods retreated from the larger galaxy. Though in the *very* beginning, I tend to think the Jedi were just a handful of monks, wandering a galaxy consumed by darkness and barbarism. Seeking, recovering, preserving and sharing knowledge (since teaching and passing on wisdom seems to always be at the core of what a Jedi does.) which naturally leads them to be universally respected as neutral intermediaries and diplomats.
I find this to be a lot more interesting than the EU's "they used to have swords...then they figured out lightsabers and changed their name to be less grey and more light" version of events. It also seems mostly in-line with the few glimpses we've seen of the ancient galaxy and the Old Republic.