So when they were travelling the commoner got infected, and he did infect the water and that made people die later, then he himself died, and the slave brought him around and mad eit spread more.
If it wasn't a simple infection but the plague they brought it in multiple places, the slave is possibly a carrier with strong resistance or not having injuries or drank the water she was still healthy.
Unfortunately the plot just tries to mess with us through shock twists halfway, and the author simply closed it in a shitty way and we have to guess, a waste of a possibly good story and our time.
I don't think so. The water was already polluted when they reached the village.
My personal view on the story is that Commoner's leg injury wasn't treated correctly (not surprising considering the age the story takes place in). During their escape, that injury got obviously worse over time. When they reached the village with those fanatic, the well was already polluted with some bacteria: could be yersinia pestis that causes plague or could be a shit ton of other diseases, like cholera, salmonellosis and many others (since the villagers died of some sort of poisoning, rather than plague symptoms). The second village, on the other hand, is suffering from what is clearly the black death (plague) and weirdly started a witch hunt...well, although burning corpses is the best way to prevent the spread of the plague, burning innocent women won't save them...oh, right, they got killed already. Anyway, stomping on the commoner's head most likely gave him severe concussions, possibly intracranial hemorrhage, and put him in a vegetative-like state for a slow death or just straight up killed him. Back to the Commoner, being only his left leg that is black, I guess it's necrosis from gangrene from not treating the injury, not a disease.
Now, about the knight/shorts guy...he kinda is impressed by the slave fighting skills. The reason he defected is up to fantasy and him saying "the country caught the attention of a strange slave" could mean that she could go batshit crazy and destroy the kingdom that put her master in that situation, starting from the brat. Also, about the hammer, like many said, it's possible that the knight was also a slave once.