In the 11th century, the Church was busy fighting heretics, and two of its greatest warriors were Leon Belmont (the warrior) and Mathias Cronqvist (the tactician). When monsters appeared, Leon requested to be able to fight them, but the church was more interested in fighting heathens than monsters, and forbid it. When his betrothed was captured, Leon had to renounce his title in order to save her. This began centuries of estrangement between the Church and the Belmont Clan.
In the 15th century, the Church employed Sypha Belnades, a witch, who disguised herself as a priest and a man. She was the church's greatest warrior and her descendants would continue to serve the church for centuries. When Dracula began destroying the humans, the Church sent an army to Dracula's Castle, but they were annihilated by the armies lead by the devil forgemasters Hector and Isaac. They sent Sypha to deal with Dracula, but she was captured by the Cyclops and turned to stone. With no one else to turn to, they sought one of the outcast Belmonts and found in Trevor a mighty warrior who was up to the task. He rescued Sypha and defeated Dracula. After Dracula was slain, it was found that Dracula's curse still remained. It is not clear if Zead was really working with the authority of the church or not, but he claimed to be a priest who was trying to rid the land of the curse. Zead turned out to really be Death, who was trying to resurrect Dracula using his former henchman Hector. He was forced to use Isaac instead, but Hector defeated both Death and Dracula.
Relationships between the Belmonts and the Church were good after Trevor defeated Dracula. It is not clear if the Belmonts worked as members of the church for the following centuries, but the church did provide them with aid.
After the Belmonts vanished, the Church employed the young Jonathan Morris, the wielder of the Vampire Killer, and Charlotte Aulin, a relative of the Belnades clan with power enough to be seen as a trump card for ultimate victory over Dracula. They sent them to investigate the reappearance of Dracula's castle during World War II and sent a priest named Vincent Dorin to meet and assist them. The two defeated the lord of the castle, a vampire unaffiliated with Dracula named Brauner, and then defeated Death and Dracula after his early resurrection.
The church likely played a key role in the final defeat of Dracula, but was only one of the players in his downfall in 1999. Their employee Yoko Belnades kept close tabs on the Hakuba Shrine which had sealed away Dracula's castle in an eclipse. Yoko was like an older sister to the priestess of the shrine, Mina Hakuba. Wary of a prophecy that involved the return of Dracula in the year 2035, they sent Yoko to investigate the intentions of the cult founder Graham Jones and sent her to Dracula's castle during an eclipse to prevent him from becoming Dracula. She failed and was stabbed by Graham, but her life was spared by Soma Cruz, a Japanese student who actually turned out to be the true heir to Dracula's power. Soma defeated Graham, but he resisted his destiny and defeated Chaos to prevent being consumed by and becoming Dracula.
After Julius Belmont regained his memories, he worked for the Church in conjunction with Yoko. The following year, the Church sent Yoko and Julius to defeat a new cult lead by Celia Fortner from creating a new Dark Lord. Julius used the last of his strength to allow Soma to enter the abyss and ultimately prevent a new Dark Lord from coming into being.
in 1475, The Bishop of Targoviste discovered the technology given to Lisa Tepes by her husband, Dracula. Considering it witchcraft, the Bishop ordered Lisa's home to be destroyed and for her to be burned at the stake. Dracula realized what was going on minutes too late and confronted the crowd that saw his wife burned in a rage. Dracula declared that the citizens of Wallachia had one year to make peace with their God before he would take everything from them. In between 1475 and 1476, the Bishop was removed from Targoviste and stationed in Gresit, due to disagreements with the Arch Bishop on matters of clerical discipline.
One year after Lisa Tepes' death, Dracula made good on his threat. His army of demons attacked and swiftly destroyed Targoviste, along with the Arch Bishop of the church. Dracula, then bade his army spread and destroy all the cities in Wallachia. With both the capital of the country and the head of the Church gone, the power of running the church and country passed down to the highest religious leader in each city; most prominently the Bishop in Gresit.
When Trevor Belmont arrived in Gresit in 1476, the Bishop was in the process of prosecuting and exterminating a train of Speakers that came to offer the city aid. Trevor interfered with those efforts, leading to a battle between him and the military branch of the Bishop's Church. The Bishop tried to have all of his enemies killed before sunset but the sun did set and he himself was then killed by the demon, Blue Fangs.
At the end of Season 1, all upper leadership and structure of the Church have been, presumably, destroyed. However, there are still low-level priests tending to Wallachian communities. The future of the Church and administration of Wallachia is in a state of uncertainty.
Regarding organizational structure:
As of 1475, the Eastern Orthodox Church was the dominant political power in Wallachia. The cities of Wallachia seemed to be affiliated with each other by a shared cultural identity. Each Wallachian city would be led by a mayor, with the Church acting as the cultural head of the country. In short, Wallachia was a theocracy led by the Church.
While not officially in charge of the running of the cities, the Arch Bishop, Bishop, and lesser priests wielded incontestable power over all the citizens of Wallachia. Even the mayor of Targoviste was terrified of angering the Bishop as he knew the Bishop could have him legally executed with a charge of heresy. The Arch Bishop was capable of excommunicating any Wallachian citizen or organization; making the excommunicated party a persona-non-grata throughout the entire country.
As of 1476, during the time of Dracula’s genocidal purge of Wallachia, the Church took a direct administrative role in Gresit under the Bishop’s rule. This new church acted as the religious head, acting governor, and secret police force of the city.
Regarding organizational values:
It is implied that the values the Church preaches are those of traditional Christianity, as dictated by the bible. In practice, however, the Church is extremely corrupt as of 1475. This corruption refers to both the Church’s tyrannical rule over Wallachia and its twisted interpretation of its own Christian values that ignore the spirit of the rules.
The Church is guilty of many of the evilest trends that real-world Christian Churches adopted throughout history: burning “heretics,” violently suppressing alternate ideas, and ignoring positive Christian values to consolidate the Church’s power.
While the whole Wallachian Church is corrupt at its high levels of leadership, it was especially so under the Bishop in Gresit. This Church developed a dedicated military branch to kill all Dissenters or even groups the Bishop personally disliked. The Bishop built this military branch by conscripting thieves and thugs as priests. This military Church had so much disregard for the sixth commandment that they not only carried weapons but had those weapons forged to resemble Christian crosses.
The Church would often use lies and misinformation to control the masses. In this way, dissenting groups were cowed and the masses could be mobilized to strike at the target groups with mob mentality. The 1470’s were thus a time of frequent superstition and injustice under the Church’s rule.
While the upper leadership of the Church was corrupt. There were decent priests who adhered to the positive elements of the Church’s teachings, evidenced by a brave priest who helped Trevor Belmont prepare holy water to save the people of Gresit. These priests still followed the rulings of their corrupt superiors, as part of the mobs. After the Battle of Gresit, the corrupt leadership of the Church seems to have been fully killed off, yet the faith of Christianity remains strong. A new Church may rise from the ashes in Season 2.
Relationship to God:
The leadership of the Church often ignored its own values and, in the case of the Bishop, had their own twisted interpretation of God’s will.
While God has made no direct impact on the events of Castlevania Season 1, it is implied to exist and be unhappy with those that run its Church.
Hell clearly exists in the animated series, implying heaven and God also exist. The demon Blue Fangs stated that God has no love for demons nor would offer any protection to a corrupt Bishop who ignored God’s true teachings. This fact is only an implication of God existing as the demon may have been speaking to torment the Bishop.
The prophecy of the sleeping soldier of Gresit proves that fate is written by a force in the world of Castlevania. It is theoretically possible that God writes the future and chose soldiers other than its own Church to fight Dracula.