I have been modifying Mothership Zeta a bit including new faces, tag skills for characters, and various armor, weapon and bug fixes.
But i have come into a problem where Elliot will attack the alien workers while Somah, Paulson and Sally simply ignore them, i was able to fix this by adding him to the same faction as the alien workers but the moment i ask him to come with me to the cryo lab he will attack the alien workers, Is there any way i can prevent this?

Why do you want the alien workers to live? I think the issue is that the alien worker faction is listed as an enemy of whatever faction Elliot and Somah are in. You could also try lowering the Alien Workers aggression levels to cowardly, that way they won't attack.