This actually plays a great role in Mendoza's progress as a moral person and assists the individual in being better prepared to deal with the social order. One can practically say that he experiences a healing process as he becomes an active part of the Guarani community and as he comes to cooperate with individuals who he previously discriminated. He learns that force only needs to be used for doing good and that it is wrong for him to associate stereotypes with particular groups. Mendoza is the typical example of an individual who comes to find peace in the place that he previously considered hostile. By suffering a breakdown he is enabled to see the world with different eyes and he comes to appreciate the individuals who he previously considered to be nothing more than merchandise. Father Gabriel's...

The fact that he is presented with the opportunity to assist them is similar to a reconciliation process, considering that he feels particularly honored to get actively involved in fighting for the people who he previously fought against.
Mendoza is finally sanctified by individuals who later experience a fate similar to his as the authorities push on. It is very probable that Joffe wanted audiences to identify with the Guarani people as they see Mendoza die.

Works cited:

Dir. Roland Joffe. The Mission. Warner Bros., 1986