They are set as enemies, they'll always be enemies. What you're able to do however is make an unofficial cease fire with an enemy squad you come across if you're being overrun by zerglings. I doubt there'll be a built in function, it will most likely be an on your honor thing, soon as you can take on the little beasties with only your squad, shoot the enemy in the back.
There's nothing saying you have to shoot them, just the fact that it's fun and they'll probably be doing it to you.
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If you can't describe what you are doing as a process, you don't know what you're doing.
~W. Edwards Deming
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