Sometimes what might make sense in real life doesn't translate well into games. In this case, maybe the emergence of a religious leader before establishment of a temple makes sense in real life and it might even work in-game. But in that case, there would need to be a set of new requirements to start one's own religion, which were mentioned already so I won't reiterate them.
As it already is, BM's religion system is unrealistic, and all the better I think because of that. However, my concern is more with dissuading questionable behavior (in this case, temporary lordships). My thought on the suggestion of a religious leader pre-temple is that anyone who is really intent on founding a religion will rush to fulfill the new requirements, then use his status as religious leader to gain a lordship to build a temple. This sounds perfectly legitimate, and probably would be.
However, just how different would it be from asking for lordship in order to found a religion? In the former case, a somewhat intangible counter of "faith" * would be used to support one's claim to a region. In the latter case it is the promise of a future establishment. In either case, the result is that the noble gets the lordship, and builds the temple.
Now, it doesn't have to happen that way. Since the suggestion here seems to be that the religious leader would hold #1 spot no matter what, then it shouldn't matter which lord builds the temple. This might reduce the number of people seeking lordships only to start a religion, but it would be hard to tell, as some people might still want to be the first to construct. And if the lordship isn't relinquished in the new suggested system, all the more reason.
*: Now I will go into the difficulties with a system that would function before the currently used system comes into play. What I mean, is, under the proposed system, which I will call pre-temple, some things might necessarily be different for fairness. In addition, I will support my claim that such a system would not drastically improve on what can be achieved under the current system. However, that only applies to the difficulty of successfully making use of the pre-temple system. I am not claiming that it might not be successful in discouraging temporary lordships more so than the current system. I am claiming that the idea on its own does not appear to justify its inclusion.
In pre-temple organization, I do not think that it should be allowed for the religion to gain any peasant followers. On one hand, that would be unfair to those religions that actually established a temple, perhaps several. They should be rewarded for having the funding to spread their faith. In addition, allowing pre-temple religions to have followers among the population is a convenient way to thwart an enemy religion. Let's say that the Theocracy of Evil is preaching Evilism and the Kingdom of Good doesn't like how several regions they took from Evil are still 100% followers of Evilism. To counteract this, many nobles of Good suddenly have epiphanies, each of them gathering the bare minimum for their religions to have sway in a region. Then the many facets of Good's various religions suddenly dilute the minds of the former Evilists, causing the Theocracy suddenly to lose influence.
Ok, so let's say that we don't allow any faith recognized by the game. Let's keep it strictly among the nobles who are starting it. First, how would the organization go, if any? Would the "founder" have options unavailable to others? If so, that provides a lot of incentive to be the founder, especially if the requirements aren't that hard. And should it be hard? Someone who is prepared to become a priest wouldn't have the highest H/P, nor that much gold, nor that much skill, usually. Maybe some do fit those requirements, but what about the soft-spoken, gentle, ascetic, prophet? The current system has the flexibility to allow for any type of prophet. It simply depends on the player to actually provide the text to make that clear.
Now, let's talk about the viability of the pre-temple system. Under the current religious system, I believe that a religion is considered no longer in existence by the game once the last temple falls. That, of course, does not stop the characters from holding onto the ideas. Under the pre-religion system, when, if ever, would the pre-temple religion "die"? In addition, would it be fully converted into the current religion system once a temple is established?
I think that if the pre-temple religion was not converted fully into the current religion system, then that means even after the last temple falls, the religion would not suffer as much because they can just start over again so long as the nucleus of "prophet" and a certain number of noble followers remain. If that is not the case, then let's look at another aspect. How would one leave this pre-temple religion? I assume that there are other nobles in the pre-temple religion. If not, then there is nothing stopping pretty much anyone from starting his/her own pre-temple religion and having it form simply by having any lord build the temple. But then, if a lord has to build the temple, that means either the prophet must be a lord, or at least one other noble has to be capable of joining the pre-temple religion.
In the former case, we get into the same deal about temporary lordships, meaning the prophet seeks to gain lordship for the primary reason of building a temple, with secondary, if any, intentions to take care of the region. Sure, one can say that in the pre-temple case there already exists a "faith" and this provides support for the prophet's position, but even in the current system, the future founder can use the guarantee of a temple as his support. In both cases, the reasons are simply there to secure a lordship.
But let's go first to the other part about membership, in which other nobles can join pre-temple. Then the question remains, how does one leave? Can he leave anytime, anywhere? Currently religions do not allow anyone to leave while indebted. I cannot say what the current system intended with that, but I will say that there should be some incentive to motivate nobles to think very carefully about which pre-temple religion to join before joining, because there shouldn't be a high changeover rate of pre-temple faiths. And then, in that case, post-temple, what would be the ranks and statuses of those pre-temple members? Surely they deserve something for sticking by the prophet for so long? But do we put all of them into one rank? Or somehow select them? Or maybe, like it is now, the #1 rank decides? In any case, it would appear to make sense if those disciples automatically became part of the religion. After all, they didn't follow the prophet all that way just to remain pagans once the temple was established. Then they would need to automatically take a certain spot, in which case, shall they go Aspirant, Member, or Senior?
Let's recap. I think that the pre-temple suggestion needs to be defined more attentively to account for many more complexities that will inevitably arise due to the attempted introduction of a new system to one that already exists. While some of the points were indeed addressed already, I have decided to explore them more so that the reasons those aspects may be valid and the ways that they had already been "solved" are more clear. I believe that this system would bring new difficulties that must first be made into a form that would both fix the supposed temporary lordship problems, and at the same time, avoid creating any new problems.
