Spain was a very Catholic state and Phillip II thought of himself a champion of Catholicism, so the Catholic Church played a major role in Spain's American empire. Church officials were royal advisors and the church also sent missionaries to convert natives to Catholicism and help regulate the activities of the settlers.
The larger goal was uniting Americans around the war effort.
Cracking down on dissent would be a negative action in support of the larger, positive goal the government sought. The government wanted a fully united public in support of the war, and so it put out the message that that freedom of speech might have its limits in times of war.
the legislative branch passes laws,
the executive branch enforces laws, and
the judicial branch interprets laws
Abraham was againgst slavery