(And I thought this was going to be a discussion about Chaosium's Apotheosis system...)
Curious and intrigueing...
For some clarification on the mention of earlier issues, 2E had a system of "Deity, Force or Philosophy". The this extent, priests of "good" worship the "force of good" and thus draw energy from that force. By the same token, priests of "honor" practiced honorable actions and draw energy from their dedication and commitment to their lifestyle (Monks, one might say, gain their powers through this later means).
At any rate, I've a few questions that you probably should ask yourself.
First, the being is more or less evolving into a deity, so at what point in that evolution does it cross-over from a being of flesh and blood to one of spiritual power?
Second, upon crossing this threshold, will it come fully into it's powers as a deity, or will it start at the bottom of that scale and work up (from Divine Rank 0, so to speak)?
The first tells you when and if the character will gain Divine Spells; The second says how quickly they become available to the deity's priests.
My opinion based on what I read: The character cannot be a Cleric of the proto-deity because, plain and simply, there is no such thing. The character can easily and clearly dedicate himself to the being, preach the being's message, work towards conversion in rp-scenarios, etc., without taking a level of Cleric; indeed, taking a level of Cleric is representing mechanically a choice made that, plain and simply, the character never had available to begin with.
Alternate 1: A priestige class of some kind that provides some form of mystical qualities without becoming too "paladinish". My own setting has a major "belief is power" premise as a primary plot-element, so providing such to me seems perfectly reasonable. You may consider a similar reason to bestow some nifty boons for his faith.
Alternate 2: If you plan to have the answers above as "soon" and "progressively", you might allow him to keep the Cleric level (and gain more) while coming up with 10 tasks from the character to fullfill in the name of his patron. The first might complete the process of becoming a deity and make Orisons available (he has plenty of slots); each successive quest completes another step of the deity's ultimate ascention, making each additional Spell Level available. In this manner, the character's numerical power might dip slightly from time to time, but not so severely that he becomes a major burden to the group.
Anyhow, just a few random thoughts...