Sektor's and Cyrax' endings will likely be canon. Also Liu Kang's is possible if he survived. He could state that Raiden did a poor job defending earthrealm because he needed the interference from the elder gods.
Sonya going rogue is plausible and the ending of Johnny Cage would still make sense even if he didn't receive insane powers. Controlling his attitude and temper in the realm of order would still be a huge improvement.
Also Noob's ending could play out if he somehow survived the soulnado, which would also introduce the chaosrealm and Havik. Kabal's ending could still play out too with the damaging of his respirator happening by another fighter. (I would really like this because of the possible introduction of an entirely new character: the doctor.) Sub-zero's and Scorpions endings could happen too. Smoke's ending is very interesting and could actually spawn a new boss.
Quan Chi's ending is absolutely canon.
However the endings of Jax, Kano, Sindel, Nightwolf, Jade, Kitana, Baraka, Shang Tsung, Sheeva, Kratos, Kung Lao, Reptile, Strykerand Cyber sub-zero are probably non-canon.