As long as there is no contradiction to the movies, EU is as canon as EU can get.
Dark Empire contradicts the movies many times. In fact, Lucas stepped in when it was noted that Palpatine told Luke that he had died several times prior to the Battle of Endor. He put in his two cents, saying that Palpatine was merely bluffing to make Luke think he was invincible, whereas the...erm, author, would it be? of the comic book had intended that Palpatine was to be taken literally.
Lucas overrules, of course.
And Palpatine was very much alive, if you think about it; he didn't have power, but his soul and life essence was still alive, and made it to Byss after traveling through space for so many years.