The idea of separating Church and State was taken up by the Propaganda Movement, in particular by Marcelo H. del Pilar who, on 15 September 1892 , denounced as abhorrently unjust the deportation of Jose Rizal to Dapitan. He said that religious reasons were used to impose political punishment for Rizal was accused of disloyalty to Spain when all he did was attack the friars, When the Propagandists clamored for secular education, religious freedom and the non- interference of ecclesiastical officials in government affairs, they were in effect arguing in favor of the separation of Church and State.
Unexpectedly, during the Revolution and the Malolos Congress that followed, separation of Church and State became a hot and sensitive issue that threatened the very unity of the First Republic. The memory of GOMBURZA was still fresh in the collective memory and the Filipino secular priests wanted to enjoy the social and political prestige of the Spanish friars they had replaced. The dilemma was to fulfill the aspirations of the Filipino seculars without perpetuating friar abuses and to remove Filipino priests from the spiritual jurisdiction of the Spanish Archbishop of Manila but still adhere to the Pope of Rome. . Aguinaldo;s presidential decree of 24 June 1899 ordered the local clergy to show their patriotism and loyalty by sending parish collections to Fr. Gregorio Aglipay and not to Spanish Archbishop Nozaleda. .
Apolinario Mabini, chief presidential adviser, penned several vital measures, which Pres. E. Aguinaldo signed, to guarantee the local clergy’s support for the First Republic specially because war with the United States already seemed inevitable. The separation of church and state issue, (its opponents won by one point in the third round ) was suspended for a future constituent assembly. When the new government had to legislate the disposal of parish funds, this was done with utmost care as indicated by the 1 September 1898 decree of Pres. E. Aguinaldo.
The reaction of Aglipay and the Filipino clergy were , to the Malolos legislators, a barometer of national sentiment. When the First Republic deemed civil marriages obligatory and religious ones optional, Felipe Calderon (who had championed the union of Church and State) cautioned his colleagues about threatening, though unwittingly, the interests of the Filipino clergy, or belittling their religious beliefs. Lest the First Republic be criticized for being anti-Catholic, . civil and canonical marriages were given the same importance specially because t the civil registry was still a function of the parishes.
As early as 1898, in a “First Manifesto”, the Hong Kong Junta already expressed “ …that the native clergy of the country be those to direct and teach the people from every step of the ecclesiastical hierarchy…” The Philippine Revolution and the Malolos Congress showed that the First Philippine Republic did satisfy the aspirations of the Filipino secular clergy. Historians say that it was Apolinario Mabini who had doggedly pursued the establishment of a national Church; in an independent Philippines, the highest ecclesiastical authority had to be Filipino. Although he did not contemplate breaking off with Rome, Mabini rejected the Spanish Archbishop of Manila who exercised his authority only in territory occupied by the American invading forces and not in the twenty-five provinces under the First Republic.