Michel - A couple of thoughts -
I'm not sure MiB is evil, I'm gonna hold out on that one.
But it's this: More importantly: Did he even meet Penny in this reality? Maybe Widmore was never banished from the island so Penny would still be there. Changing the future didn't bring joy to all of them. that really got me to thinking.
Obviously, lives up until the point of being on the plane pretty much played out exactly as the other alternative lives. Locke's still in a wheelchair, Jack's dad is still dead and had gone to Australia, Kate's still in handcuffs, Sawyer's still a con, Sun and Jin are still on the outs, ect. Why would 2 people have different lives - Hurley - considering himself "lucky" and Desmond - being where he wasn't originally? Also - Rose to a certain extent - being the one to reassure Jack and not the other way around.