I want to know what's up with all of the Assassin hints. Corrupted, the fly edited in on that cinematic, etc.
As for your Morpheus theory, it's definitely possible.
The only problem is that the HvCFT signals were not comeing from the real as everyone originaly thought. They were being rebounded in the real and back into the Matrix but there source was comeing from inside the Matrix its self. So the SIM we see now is defently not Morpheus. (I think thats what you were sudgesting correct me if im wrong)
Heh, are we headed for a case of "Will the real Morpheus please stand up?" if Morph himself should come back to the Matrix, or be reported having returned to Zion...