Evidence that Widmore is serving Jacob by timeisrelative

1) My favorite piece of evidence occured in season 4 during an exciting confrontation in Widmore's penthouse. Ben and Widmore's conversation was so cryptic, it felt like it was riddled with clues to answers when we have yet to know the question.

Widmore told Ben, "I know who you are, boy. What you are."

Widmore emphasized the 'what' which was a bit perplexing at the time. Now we know. Widmore was acknowledging that Ben has been infected and is being controlled by the monster. Ben himself understandably accused MIB of being a 'what'. MIB corrected him, "I'm not a what, Ben. I'm a who." Even though MIB later admitted to no longer being human.

2) We've always been led to believe Widmore wants to exploit the island. But that was only Ben's point of view. And Ben was being manipulated by MIB. Widmore is a faithful servant of Jacob. He was ostracized for connecting with the outside world. That's what Jacob wanted, to bring people to the island and use it to further mankind.

3) Widmore didn't want Locke to die. This would obviously counter MIBs plan.

4) Widmore claimed Jacob wanted Ben to kill Baby Alex. Infanticide sounded a bit cold for Jacob which made us suspect Widmore wasn't acting in Jacob's interest. But if Jacob knew that Alex would literally be the death of him, Baby Alex might be an acceptable loss.

Despite MIB's treacherous demeanor, I'm in the group that believes MIB and Jacob are neither good nor evil. Jacob believes the island can help mankind. MIB believes the island is too dangerous for mankind. MIB is protecting us from ourselves. He may be willing to kill, but it's for the greater good. Actually, I believe MIB is aware of the flash sideways and knows that the death of someone in our initial timeline doesn't mean they're actually dead. Like our pal Charlie said, "I am dead. But I'm also here."