No, you just have to ignore them. All the muds left in RuptureFarms get killed when you leave the first time.
I haven't actually tried to get the super-bad ending but I don't think you have to kill all the muds. I think you just have to save less than 50 as there is no super-bad ending, just the bad one. Correct me on this one if I'm wrong, people.
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Spending as long as I do here, it's easy to forget that Oddworld has actual fans.
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