Historically, the Church has existed in one of two conditions — tolerance or persecution. I use the word tolerance because even in times when the Church is seemingly in power, its fundamental principles come into direct conflict with those who are primarily motivated by money and power. I can't begin to count the number of times bishops came into conflict with Christian kings and emperors. Even under the best of circumstances, bishops were exiled for standing on principle. Also take a look at 21st century America where a lot of people these days are offended by the words "Merry Christmas."
In a fantasy setting, therefore, one must make a decision as to which condition the Church is in and if in persecution, what kind. Prior to the Roman Empire becoming Christian, it was largely illegal to be a Christian. This situation usually played itself out by trying to force Christians to make sacrifices to images of the Emperor. Failing to do so was seen as treason. There were periods when Rome actively sought out Christians to put them to trial, and there were times when it passively did so. Those killed were called martyrs — witnesses. Christians would take and bury these martyrs and then hold services around their graves. This is the origin of churches being named after saints — when churches were allowed to be built, they built them around those places where martyrs were buried. Thus, that was the church of saint so-and-so who is buried underneath. To this day, Orthodox churches keep relics of saints inside their altars in memory of this practice.
Both the Chinese and Japanese persecuted the Church as a negative foreign influence. The revolutions in France and Russia persecuted the Church as part of the old order. Although Islam has seen Christians as "people of the book", it still persecutes Christians as infidels.
In terms of organization, the Church has four orders of ordination — the laity (yes, baptism is an ordination!), the deaconate, the priesthood and the episcopate. In terms of the clergy, bishops are administrators, priests are teachers and deacons are servants. For about the first millennia, one was ordained to a particular order for life. In modernity, one becomes a deacon, then a priest, then a bishop. In the ancient Church, all orders allowed married clergy — though one was not allowed to marry after ordination. In the Orthodox Church, this still holds true for Deacons and Priests, but all bishops must be celibate. In the Orthodox Church, women have never been ordained to either the priesthood or the episcopate; however, they were allowed to become deaconesses. This practice existed through the ninth century and has seen some movement towards restoration in the 20th (Greece has allowed them to be ordained for women's monasteries).
For the purposes of a fantasy RPG, the order of clergy best suited for adventuring is the Deacon. Bishops are tied to a city. Priests are tied to a parish. Deacons can be tied to a Bishop. Thus, a Deacon can be ordained by a bishop for the purpose of adventuring. Thus, the class has a built in patron which can be a source for adventures. This patron can be as meddlesome and demanding (or not) as a Referee wishes them to be.
Using this set-up, the Cleric class can come in three flavors, only one of which actually does any adventuring. This severs class level from church hierarchy. In other words, a 1st level Cleric who is a bishop would have authority over a 9th level Cleric who is a deacon. So, priests and bishops need not be any higher level than 1st to have the kind of respect and authority that their positions demand. Thus, it is possible to have a fantasy world where divine magic has very little broad impact. Spells like Raise Dead would be extremely rare, if accessible at all.
In terms of the end-game, a Deacon could still build a stronghold. In a church structure where they are ordained as a deacon for life, they would attract a priest to fulfill that role. Otherwise, they could be elevated to the priesthood or episcopate and take over. The former, however, is more representative of the historical church. Monasteries are led by abbots — which are not necessarily priests. Thus, a stronghold built by a deacon would see the deacon as the spiritual leader and any priest that comes to serve fulfilling that particular liturgical role.
For those that use such things, Domains can be explained by way of religious orders dedicated to a particular saint. The Domains would reflect the life of the saint and their path towards God. Thus, Domains like Chaos, Evil, Madness, Death, etc. need not be left out of a game. For example, St. Paul persecuted the Church prior to his conversion. Thus, a fantasy religious order dedicated to a saint akin to St. Paul might have as one of their Domains Evil or Death. St. Paul transformed his emnity towards the Church into evangelism across the Mediterranean world. Thus, clerics dedicated to his order would be expected to transform the Domain of Evil or Death in a similar way.