It is officially a non-canon episode but only because of the existence of Alien Force.which obviously contradicts a lot of what happens in GBaGR.
For me though, it is the canon ending to Ben 10 in my heart (following Secret of the Omnitrix), or at least the Ben 10 which Man of Action and the rest of the writing team were working on. I feel that it is just so much more satisfying than any other finale of the other shows. We see Ben's summer finally ending, a return to normality for him along with an introduction to his parents, Ben finally managing to destroy Vilgax once and for all, and his secret being revealed to the world. The Omniverse finale was decent but as cool as it was to see the creation of the universe, it lacks the personal connection to Ben and his growth which GBaGR does so well.
I think that it was a fitting conclusion and I imagine that the sequel which the OS team were originally working on would've expanded on this and led up to Ben 10,000. I see Good Bye and Good Riddance as the original team showing their own ending to the series, even though it ended up being non-canon.
I do believe that Ben keeping a secret identity would be better for storytelling purposes though, and I wish that Alien Force had actually done that before his identity was revealed at the start of Ultimate Alien.