Excommunication was theoretically an extremely serious punishment, but in practice it was used with surprising liberality even for very minor offences.

Pedro Calderón de la Barca, the famous playwright, was excommunicated twice for something quite trivial: not paying rent. In 1617, Pedro Calderón was a student in Salamanca, and not in phenomenal economic shape. That's why he wasn't able to pay the house he and his cousing had been renting. In December that year he was excommunicated and thrown in jail. In order to pay the 150 reales he owed to his landlord (who was a priest), Pedro had to sell his cape, which gives you an idea of how poor he was at that time.

In June 1618 his cousin and him were, again, unable to pay rent, and they were excommunicated again. The procedure was more or less the same, and the excommunication was not lifted until the debt was paid, which took them some days and some pawning.

These cases were extremely minor offences, but the example present in Don Quixote is far more serious. Exercising violence against a member of the Church, a prince of it no less, was something that would have the punishment of excommunication lata sententia, which is to say that the trespass itself automatically carried excommunication. For example, in book VI, title XI, chapter XXIII of the Decreta, edition of the year 1591, we find the following:

If one hits a cleric without my command, or not in my name, shall he be excommunicated. [...]

Whosoever lacking my mandate would exercise violent actions on a cleric, shall incur in excommunication lata sententia.