On the contrary, Frankie stated at the ODST launch event at Seattle Center that all of the Halo: Legends stories are canon, save for one, which will be the one by Toei.
As for some of the environment and character designs which is what really has been irking some fans, I'd just like to think of them as "artistic interpretations." From what I uinderstand though, the overall silhouette of things may still be canon.