Well, I arrived at that decision surprisingly quickly. And it was like a weight off my shoulders when I did.
As you know, or at least can see from five minutes in my archives, I've thrown away days of my life researching and trying to come up with a religious framework that is not Crystal Dragon Jesus, but adequately leaves room for the spells and class features typical of the cleric, which is loaded down with a lot of implicitly-middle-class-American-Christian ideas about both gods and holy men. Some may enjoy that, and far be it from me to condemn them, but for me it always seemed a little... intellectually lazy. So I had some cognitive dissonance to work through.
It has been less of a challenge and more of a vexation, frankly.
So, I got to thinking, something has to give, either I have to learn to stop worrying and love Crystal Dragon Jesus, or I need to stop trying to fit his vaguely-cross-shaped peg into my round fantasy hole. Apart from which, I think it's just not terribly compatible with my largely non-theistic (though not atheistic) take on the world... not to sound hidebound of course, but I just do not give a damn about the existence or worship of gods one way or another, and there's nothing worse for a story than not giving a damn about its subject material.
There is something that does come a little more naturally to me though, in terms of the human relationship with forces that are, by and large, beyond it: the sort of "virtuous pagan" attitude that seems to come standard for the good guys in Tolkien. Of course I come to it for different reasons-- him writing an intentionally Catholic work, and me, as I said, just plain not being arsed about gods in the first place. But that same sort of attitude-- reverence toward nature/the universe, song, belief in good and courage and stuff... that I can write for. Now, a druid (in the fantasy sense of the term, at least) or a witch, I think, can reconcile easily with that worldview, but not so much a cleric.
I think, despite my initial reservations, that just passing most of the spells that aren't already duplicated over to the Magic-User is probably a good start. Particularly if I just go with Wound Points and Vitality Points-- I think VP/WP reduces some of the burden on spellcasters to always have healing prepped (especially if healing only works on WP) because VP regenerates comparatively quickly.
The big mechanical problem I found myself stuck on, then, was what to do about the other vital function of clerics, the one which Mike Mornard and his friends originally demanded the creation of the Cleric for: Turn Undead. I've seen some retroclones make it a spell as well (usually a 2nd level one), but I wasn't sure if that was the best option. But I was concerned both from a gameplay perspective (that making it a spell might make it too scarce comparatively, making undead particularly nasty and killer opponents), and a thematic perspective (just what is the spell doing?).
To be honest I sort of always thought of it being like the "True faith" feat or advantage in many other RPGs... which... honestly doesn't make much sense given that paladins tend to be both more zealous in general and less effective at turning. Of course there's the 3.5 answer: that it's somehow channeling a positive energy that's anathema to undead... but the check for it is weird, in that case, isn't it?
But then... the fact that Energy Drain is one of those other things that just bugs me means undead lose a bit of their teeth in the first place, maybe I don't need Turn Undead so badly. So that was it. Kill the Cleric, pass on its spells to the Magic-User. My life is simpler now.
Of course this doesn't mean there isn't religion, but ditching the
character class explicitly focused upon it means there's less of an
obligation on my part to try to force together something that isn't
crypto-Christian but where there's still somehow a militant order of
priests that use maces and wear armor and heal and part the ocean and
scare the undead and stuff. If I need priests or a temple for a story,
or even if I have a player who wants a religiously-inclined character, I
can make up something that works for the scenario I want to provide or
the story they want to tell. And that's... extremely liberating.