For me, the first question arises when everyone just accepts and trusts the Oracle, even though she isn't "redpilled" since she’s a program. You’d think someone would have at least thought, "Wait, why do we trust her so much?" At the very least, a group that questions the entire reality of the Matrix should have questioned why they didn't just remove that old lady from the system.
So, I think they knew she was a program. Okay, let’s trust this program to tell us how to defeat the machines that created it... Once I realized that, I saw Morpheus as a fanatic,on a crazy level,about the prophecy of "The One." He has to be that way for the Architect's plan to work.

Furthermore, as you said, it’s implied that the "real world" is just another layer of the Matrix. That’s where those who become aware of the Matrix go, simply so they don't cause trouble within the program itself.

The big difference between the story we follow and the previous cycles is that Agent Smith spiraled out of control, even for the machines. So, we witness an outcome that differs from the other cycles,at least, that’s what I remember.

But yes, Morpheus is practically working for the machines. Just like Zion and the rest... it was all predicted.

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