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Maybe instead of flags, it can be some working mudokens, or maybe just Alf  , that Abe has to save, but he has to make sure that none of the other sligs can see him with the help of the shadows or something like that. Also, I don't think that it would be too bad to have the sligs use their incomprehensible voices like in that one cutscene from the original game since there are hardly ever two sligs put together in the same room anyways.
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Ok, once the player finds Alf, he/she needs to escort him out of the base without getting Abe or Alf killed. If either of them die, the person playing as Abe looses.
It'll be harder having to rescue Alf because now you have to worry about keeping two things alive (Abe and Alf). That's why having a flag would be easier.
You also have to remember that the Sligs are being controlled by Human players. Imagine trying to escort Alf out of the base while having to deal with real people.
They could try to limit the mobility of Human controlled Sligs, but it would be boring being limited to two screens.