Read the comic here.
I think a "real" fight between the two Morpi would probably go a lot like the way things went in the strip. Endless Morpheus would be bemused for a bit, then just wave his hand and Matrix Morpheus would be toast. (Sort of like the Punisher going up against Galactus or some other cosmic power. At some point, he's just going to be vaporized, fan-base or no.)
Regardless, I had to shut down the fight quickly. I only have two weeks to transition into Advent Madness, and I do tend to ramble on.