I see him as misunderstood.
He's a ladder climber to be sure..and he's smug. But he DID show that VERY personal tape of himself as a young boy (something he'd rather keep a secret because it's so humiliating to him) to Scully for no other reason than TO HELP HER.
He didn't even know Scully at all and yet he gave that sad, sick aspect of his childhood to her as a kindness. He didn't want her to get caught up in the same sick web he'd been trapped in and ruin her life. That was decent of him and showed that he is willing to make sacrifices for someone he doesn't know.
I think he has good reason to dislike Mulder. After all he feels that Mulder was taking advantage of his mother's deluded state of mind for his own gain. I'm sure it's been all around the FBI that Mulder often does this with people.
Mulder did that with Barry when he had hostages. He fed into his sick world veiw for his own personal gain risking the lives of everyone there. He's used people like this so many times it shows that he's often dangerous to those he should be helping.
Calling Spender, "The son of...the prophet" probably didn't help in constructing any bridges. Neither I'm sure did squashing that pack of Morley's in his face when he was after all guilty of NOTHING. Spender's going to be tempted by "THE DARK SIDE" but he'll pull out of it for season seven.