Hmmm... that's a bit of a tough one. There hasn't been an official statement either way since the purge. But, there was a statement a little further back specifically about the novelizations of the films being canon as long as they didn't contradict the films. But, this apparently was rescinded as Wookieepedia isn't treating them as canon, but as legends.

I would say, based on the information we have now that the deleted scenes are not canon. I think the easiest method to approaching the purge is to assume total annihilation of the old EU. Therefore, only the movies and Clone Wars are canon, along with (most) newly published material starting on that date.