Laurence Fishbourne, in an interview that came out on TV around the time of Reloaded opening, said that Morpheus was crazy. Not as in “insane”, but his quest, his belief in Neo and the end of the war, is making him somewhat of a “religious zealot.” And, Fishbourne added, “In reloaded you get to see just how crazy he is.”
Don’t forget how he looked in the beginning of M2, when all the captains were gathering, and Morpheus, Trinity and Neo arrived.
Morpheus just melting out of the darkness, his shades shining, looking somewhat like an alligator. He’s not an agent or a program.
A once scene shot, which won’t burn itself onto the retina, because it happens in an instant, is, as I see it, more a scene-piece, than a real hint.