Think about it, Lionel never does ANYTHING without an ulterior motive or expecting something in return.
There were some clues. Like in Void as he says "Have a good evening *CLARK*" as he goes out the door with Martha.
Also the fact that he clearly threatened Jonathan in the 100th episode with the picture in the barn. With Jonathan he could show his true face, because of the bad blood that Jonathan has for him anyways.
He knew he had to play Clark (for his abilities) and Martha (whom he has the hots for) in just the right way. He doesnt act like the true MB that he is to them.
TRUST me.
Once a MB, ALWAYS an MB.