I am late to the game and found that when using nightsisters on Rebels they have the ability to completely clear the Plague stacks off with no issues. Not sure if this has been reported or if this is a feature the rebels get with no penalty but it would seem if the debuff is locked that would mean it couldn't just be cleansed.
In general the rebels buffing and over buffing seems a bit unbalanced too
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Same way that ewoks beat the empire with sticks and rocks, because the plot needed it to happen
Could it be the Plague is expiring naturally? A single stack only lasts for 3 turns, no matter how much health the afflicted unit has.
Thanks EventineElessedil for the quick answer.