The roaming cows are a good illustration of how deep the chaos is in the town of Salem once the witch trials get going. Under normal circumstances, no one lets their valuable cows roam in the streets. But Salem has been turned upside down with the witch trials.
Cheever makes this comment because he has been required to arrest people accused of witchcraft. And he observes that there have been so many people arrested that there are many farms abandoned therefore the cows are just roaming around with no one to look after them. Their masters are either dead, in jail or so caught up the the hysteria that they are in the courtroom everyday.
The witchcraft hysteria in the town of Salem has reached a fever pitch. There have been so many people accused of witchcraft and so many people in the courtroom every day that farms and livestock have literally been abandoned.
The social order of the town has fallen apart; reality is now defined by who is a witch and who is not. The members of the court and the people in the town become so caught up in the witchcraft hysteria that is takes priority over everything else, it sets the new order in town.