Even if he is Skynet, humanity is dead for the largest part, the rest lives in a medival society (no electricity, computers or internet)...we also know that this genetic bio weapon on the other isle would very likely infect the rest of the humans sooner or later, even if u ignore MC's group, do to the ressource shortage...so there isn't much additional harm he could do, if want the humans dead he just needs to lay back and watch.
As for the helping, he was made to be helpfull and he is stuck with the MC if they want it or not, so cooperation seems to be the best way, he also wants the MC to integrate the 2nd AI which could end deadly for him...so being helpful is in his best interest.
He probably also don't want to watch humanity die for a second time, or maybe he just thinks helping the humans is in his best interest of long term survival.