There are the things we learned about the other side--the different rules, the different set-up, the different perspective--and then there are the things we learned about Walter Bishop and William Bell. So, no, Bell is not the enemy, but he's sending the shape-shifters over to our side just to appease Walternate, more or less. He's still there to prevent a war of the worlds from happening... but I don't think he's been successful.
You see, Walternate looks like he's not willing to let go of the fact that Peter was kidnapped twenty years ago. Sure, the impact of Walter nabbing his alternate son had a much bigger impact on the other side -- the "soft spots" really altered the laws of physics over there, it seems, which explains Fringe Division being run by soldiers and the scary idea of "quarantine amber" -- but it's more a personal vendetta than anything. That surely explains his plans to destroy our world so everything will go better on their side. I think all he wants is to kill our Walter, and he will stop at nothing to achieve that, even if it means using Peter.
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