Answer:
There were alternatives for justice in the middle ages, and in fact there were more than there are today, because their were alternate courts, at least for some people.
The courts available for members of the nobility were run by, and for, members of the nobility. The people on trial were nobility, and the people trying them were nobility.
This was not true for serfs. The people trying the serfs, if they were not nobility were at least paid by nobility (change came later in some places). But, in many places, such as England, if a man could read a particular Psalm, designated by law, then it proved he was literate, and should be tried by a court run by and for clerics.
The clerical courts were judged by clerics and clergy. Remember that these people were not members of the nobility, necessarily, but came from all levels of society. For example, Pope Leo III, who crowned Charlemagne, was of humble origins, and Thomas Becket was the son of a merchant who bought and sold cloth in the Cheapside area of London.
The result was that a serf who learned to read could get a much fairer and merciful trial than one who had not. (One wonders about the effect on literacy. I would bet criminals taught each other to read.)
The idea that church trials were unfair and produced harsh justice may be a product of the later times, to a large extent. There are records of criminals in Spain, during the Spanish Inquisition, confessing to belief in heresies so they could be tried by the Inquisition instead of the normal criminal justice system.