I did a job with Lucasbooks back in the mid '90's. I asked the guy I was working with from LB about the validity of the EU stuff and even back then he said "If George didn't write, shoot, direct or produce it - its just fan fiction."
There have always been guidelines the EU writers had to stick to - certain topics or situations that could not be covered. Simply because they would be stepping on the canon's toes. Thats a pretty clear line drawing in the sand right there.
I never assumed SWTOR was canon. It is speculative fiction about the origins of other fictitious worlds and events. It doesn't hamper my enjoyment of it.
To me the whole situation is like the Star Trek novels - no-one ever assumed they were canonical to that universe. Its not really any different here. Except of course that many SW fans grew up on the EU novels. And I guess that is where the sense of betrayal comes from. As one who saw the first movie in '77 as a 12 year old I personally always looked at the EU as 'parallel universe' stuff.
(The LB project I worked on was a re-telling of Episode 4 using screen-caps - kind of like the old photonovels).