Given the shadow war approach the game seems to be taking, the local forces could be made hostile too. There is a possibility of stealth/non-lethal gameplay, and that could be expanded to local forces as well. Fighting aliens and their henchmen with lethal force, but carrying stun weapons in case the local forces attempt to engage you and the aliens. There was also talk about intelligence gathering being a requirement to missions, and that could be used to tag local forces are enemies or not, and maybe even allies. That way, if acting on weak intel, you might be required to investigate to see if the a unit is a local force or an alien force before killing/subduing. If acting on strong intel, maybe you are able to arrive dressed in their uniforms or something and fool the local forces to work with you.
Time will tell!