I'd posit that this was the original intent for the vanilla game, and got changed during playtesting. I suspect they chose to give to the Apostles, via the Evangelize Belief ability, the purpose originally planned for additional Great Prophets.
If I'm right about the above, then it's unlikely that they will put more Great Prophets back into the game. If so, I would still like to see the developers create a use for Great Prophet Points that last throughout the game. Technically, all great people points have the same issue, it's just that the Great Prophet Points obsolete so much earlier than the others, it's much more noticeable.