I think Scratch being mentioned hints towards one of two things : Either Durai got usurped after the humiliation of the tower attack, as, although it can't been seen as a victory for either side, Durai was humiliated in the way he dealt with the situation, and Scratch was probably in line to replace him after her deeds during the initial outbreak(getting the mallers out of the prison). However, not everyone would have agreed with Scratch's leadership and therefore they became "runaways".
The other possibility is that Scratch is now working with the colony, having left the Mallers after the attack on the tower or another event we don't know about, and is now working to recapture the deserters after the coup, the only reason I feel this is a possibility is that the two mallers/colonists were surprised that Lizzy had a gun, and I don't envision such tight restriction on guns in the mallers camp in comparison to the colony, who had a very tight lockdown on weapons, and therefore guns would be easier to come by for fleeing Mallers.
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