What system control people's freedom in the middle ages?

Mostly, control over the ordinary lives of most people came from laws and customs pertaining to the manorial system.

The Church exercised some control over people, but this was not usually exercised unless the people were either (1) both important and in conflict with the church (as in the cases of Henry II of England and Henry IV of the Holy Roman Empire) or (2) part of a heretical group large enough for higher Church authorities to notice.

The popular view is that the medieval Church routinely burned people at the stake for witchcraft and excommunicated people in order to prevent progress in science, but these problems did not really develop until about the time the Renaissance started, and were not large scale until after the Middle Ages were all over. Contrary to this view, the Church provided Right of Asylum, which in many places meant that a person seeking asylum could not be removed except for certain serious crimes, and then only after having time to repent and be forgiven (often six weeks); and in other places, the person could not be removed at all, even if that person was a felon sought by agents of the king. Also, the Church had Benefit of Clergy, which meant certain people would be tried for crimes before special courts run by the Church, more lenient and without torture, and these people were not just clergy, but, indeed, anyone who might become clergy, including students, and anyone else who could read.

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