This is a question I'm more concerned about than who's side is Widmore on. There is a chance that there could be another familiar face on that Submarine. Perhaps, he's broughten Walt or Aaron, or maybe he's broughten more mercenaries to join MiB's team or to fill out Team Jacob for more of a fare fight.
There is also the chance that his sub was followed. We all know from the scene where Charlie died that Penny has just as many contacts as her father. Who's to say that Her, little Charlie & Desmond aren't right on their tails. I'm sure Penny has people informing her of her fathers every move. And when he boards a sub of all things, I'm certain she will take notice. And with Desmond knowing that his friends were back on the island, and what happened last time Widmore went looking for it. He might feel obligated to try and prevent another massacre.