This makes sense?
"The body can not live without the mind."
Morpheus tells us this in the beginning. It's true! Why is it everyone says X was a program whenever? Even when Neo was in mobile ave, his body and mind remained in tact. One can't live without the other.
No, Seraph is not a former one. He is a program that somehow came to work for the Mero. Hence his 'prodical son' and 'Judas without wings' comments. He protects that which matters most - the Oracle. Whatever deal Seraph and Mero had going caused Seraph to loose his wings before Reloaded. He clearly keeps some abilities though.
In the Matrix, Morpheus looks at that man by the elevator, who nods. That is Seraph. A Seraphiam can change its appearance depending on the situation. This also backs up Smith's "I remember chasing you was like chasing a ghost." Seraph, an exile then, escaped the Agents with his cloaking ability. Seraph fought Morpheus and granted him passage afterwards before the events of the Matrix.
In Reloaded, Neo meets a wingless Seraph. (This is pure speculation. I believe Seraph worked as a double agent to take the Oracle's eyes for the Mero. The Oracle won him over, and Seraph choose to stay with her. "He has protected me for years," says the Oracle. Seraph looses his wings to the Mero for breaking the deal. Hence his shell program appeared different in Reloaded. Everyone assumes he is weak enough to kill. The bouncers say "Hey, it Wingless.""I get it. You must be ready to die cuz the only way you're getting in is over my dead ass." Seraph, now weaker, uses the backdoor key he had in his service with the Mero to hide the Oracle from the Mero's henchmen. He fought Neo to be certain he was the One because he couldn't protect the Oracle like before.)
Seraph still holds some of his abilities though. His ability to detect when an enemy is coming in advance. His appearing seemingly out of nowhere in Revolutions at the Hell Club entrance. He has aswome fighting skills and the ability to protect the Oracle for years. The other exiles reconize him as stated above. The Trainman too is frightened out of his mind meeting the assasian angel and flees for his life.