AFAIK, at this point, everything but possibly Justice League is still canon within the DCEU, isn't it? Is this just about Snyder's changes to JL or more than that?
Movie series "canon" is a flexible thing. Later sequels often ignore earlier sequels (Highlander, Halloween, Terminator), play fast and loose with chronology or continuity while pretending to be consistent (Universal Monsters, James Bond, Planet of the Apes), or simply miss the point of the originals (e.g. TRON Legacy claiming Kevin Flynn was some kind of champion of open-source software when he was actually trying to get the money he was owed for his stolen creation).
So there's no reason a future film couldn't cherrypick bits and pieces from both versions of Justice League and try to split the difference. Something similar happened in the movie Godzilla: Tokyo S.O.S. It's set in a continuity that includes the first Godzilla and Mothra movies but diverges from the original timeline afterward, in that there were no Godzilla attacks between 1954 and 1999. Yet at one point, a returning character from Mothra recognizes Mothra using an attack that she only used in 1964's Mothra vs. Godzilla, which never happened in the movie's continuity. It could be that the writers simply forgot the continuity discrepancy, or it could be that they cared more about homaging past movies than being nitpicky about continuity.