Thor has been shown to be both strong and weak, whereas Apocalypse was only weak to the Phoenix Force. Quicksilver landed a few punches on him but Apoc was still fully concentrated and able to stop him after a few seconds. Apoc was also able to stop the combined powers of Charles (mental attack) Storm and Cyclops' energy/electricity blasts, and Magneto's constant pieces of metal. His throat being slit was healed instantly. I thought his skin would have been stronger than that but it doesn't matter as he recovered swiftly. The only thing able to stop him in the end was The Phoenix Force.
Now onto Thor, in the first movie he was able to kill loads of Frost Giants by smashing the ground with lightning and able to destroy that big creature with ease. He also defeated The Destroyer which I don't really understand but he seemed to do it with relative ease when regaining his powers. He didn't seem to strong in The Avengers but there was a city full of people so it's a morals game of which would make him seriously depowered. Thor 2 he was beaten by a being with some kind of energy instead him, perhaps a portion of The Aether, at least I hope. This being deflected Mjolnir like it was nothing. He was throwing Thor around and beating on him like he was nothing. I won't talk about the Malekith fight because the way it ended was pretty pathetic. However he did match him when he had the Aether energy which was impressive.
Ultron also smacked him around for a bit before Vision sent him flying with Mjolnir, I would like to think he could have easily took control but I'm not sure with this version of Thor. Later on he did destroy a small country (sokovia) with a lightning bolt.
I can't see Apocalypse's fields stopping Mjolnir so if it was a bloodlusted fight I would think that Thor could smash his head in or call for Thunder whilst Apoc is recovering and then disintegrate him before he knows what's happening. If a knife could seriously damage him think about what the hammer could do.
Morals off = Thor win
Morals on = Maybe Apocalypse
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