Since I highly doubt that Bethesda is capable to do what BioWare did in Mass Effect, there are only two options for that. Neither are good though. Of course they could just say "That's canon, that ain't" which would obviously upset the Community. I for one am a true Nord and all those traitors are to be brought to justice (all those 'essential' NPCs will have a proper execution once the CK arrives). Others like a buddy of mine stayed true to the Empire and took down the Rebellion because 'he likes romans'.
The other thing is; they could create another Dragon Break like they did in Daggerfall which would be entirely stupid (not even now it makes sense what they did back then).
What do you think and which is the best scenario? Maybe you got some ideas how they could resolve it without being stupid or upset the fans.