I don't really understand the confusion. It's left opened who defeated Taven, but I doubt it was Raiden. MK Armageddon's konquest is canon and it ends after Taven defeats Daegon and Blaze is unleashed. "Now face me in Mortal Kombat" he screams as Taven walks through that portal swinging his sword. Epic! But the actual fight between them is just an extra scene, so Taven never defeated Blaze. Shinnok corrupted the competition between the brothers and informed everyone of the prize, sending his own clone to lead his army, somehow being aware that the timeline will be reversed. In my opinion, it was him who enslaved Blaze to the Dragon King's priests in the first place, as he admits to Daegon in the konquest mode: "All things have lead to this moment". The reason for his actions was to ensure the death of Shao Kahn. It was never stated, but it's a fact that Shinnok attacked in both timelines AFTER Shao Kahn was defeated. Why? It must be that, despite all his insanity, Shao Kahn would have helped the Elder Gods and Raiden if Hell had attacked. As long as Outworld had him as Emperor (10.000 years) Shinnok never attacked the realms. Sure, he didn't have the Amulet, but Bi Han brought it to him even before MK1.
It's just a theory of mine, but I think that Shinnok had been stopped by an alliance between the Elder Gods' warriors (Raiden and Fujin) and Shao Kahn all those thousands of years ago and I'll continue to believe that if not disproved. It would make Shao Kahn a warrior a lot more intelligent, as he seeks the power of the realms, but not their Apocalypse.
With Shinnok and Shao Kahn gone, I doubt that there's any reason for Armageddon anymore, but I would love for Taven and Daegon to be playable in the next game.
John Vogel stated that Taven did not defeat Blaze, but Shao Kahn did. It's possible that other events surrounding the end of MK:A are kept canon, as you said.
My point is based on Raiden's first vision. We know someone defeated Taven, but we don't know who or what moment after or during his fight with Raiden (since he appears fighting against Raiden, we can say that the events that led there did happened) he was defeated/killed. As Raiden had this mission, his first vision (thus last happening), a pact with Kahn, future winner, and confronted him in the end led me to the possible idea that he defeated Taven. Not konfirmed, obviously.
[...]
Though once again in a ridiculous portrayal on MK:A, Shinnok for sure was the mind that gave the ultimate traces to the battle of Armageddon.
But I doubt he had any knowledge of the possibility of the timeline change.
His main plan was to take out Shao Kahn and weaken Earthrealm, but it wasn't possible on MK3. He planned that because, as seen on MK9, he wanted to invade Earth AND Outworld, which would be easier without Kahn and without ouro defenders.
As Liu Kang defeated the Emperor and made him withdraw his forces, I believe Shinnok's plans had partially failed, and for that reason he decided to invade Edenia, that was freed from Outworld, instead of invading Earth at first, since our heroes were intact and Shao Kahn still existed, making harder to invade Outworld. On the current changed timeline, his plans were a success, since Kahn was killed and Earth heroes were not only defeated but allied to the Dark Lord.
[...]
IMO, Armageddon is not avoided.
It was never caused by Shao Kahn or Shinnok. They only accelerated the process and the later has corrupted the quest, not created the end of all things.
As stated, Armageddon is the end of all things caused by numerous kombatants tearing apart the fabric of reality. While Shinnok, mastermind of corruption, and Shao Kahn, warlord, are out of the scene, new fighters appear and mostly important, Raiden follows the very footsteps of his alter ego on the unchanged timeline, and he surely helped to that ending, he even made a pact with Darkness.
Now he is much more angry, capable (he is indeed Earthrealm's protector, he wasn't on the unchanged timeline) and powerful (possessing the Amulet). At the same time, more heroes and villains (+ kombat) and we don't know the current status of some threats (like Onaga).
The quest was a solution, no matter how they smash the flowers, spring is still a truth.
Obs.: Of course Shao Kahn wants to destroy the realms. It's exactly what he does at the end of Armageddon, according to Vogel.
Sent from Earthrealm. Please, beware the Thunder God!