The main problem I've found with CH, and to be honest, most of SoE/Verant's problems (This is partially opinion, but it's mostly in reference to the massive item and stat point inflation that occured to compensate for the difficult raid mobs) is that they were all implemented with little to no foresight in mind.
This may sound a bit farfetched, but it's an age old problem that's deeply rooted into the game itself, and unfortunately has been built around and upon, rather then fixed.
Basically, if CH is taken out of the game, things will fall apart. Raids will be practically impossible, and clerics will be constantly puzzled as to where all that mana went. And it's not so easy as just retuning the mob dps (across the board, might I add, which would make the best of us go insane), because that will in turn change other balances.
I remember when we (The GM's at the time) brought up the original idea of removing CH, and quite frankly, I support it, if it were indeed a possibility. I think it's stupid to have one end all, be all spell that is obviously one of the class's sole spells. Unfortunately, these balancing issues arose again, and it'd be more hassle than it's worth.
Now, I'm going to assume that this entire issue lies within the realm of raiding high end mobs, because as far as I'm concerned, and from what I know, HoT's work fine in pretty much everything but high end raiding (and by work, I mean a quicker alternative than CH but more mana effective (I may be off on this part, I don't remember the specifics regarding mana use vs. healing output for the various spells))
Anyways, on the actual topic at hand: Heals over Time. What role are they meant to play? I always viewed them as a spell that could be used to guarantee that over a certain period of time, your tank will have some health, giving you some leeway in between Complete Heals (which I still loathe.) But unfortunately, as the mobs you fight get increasingly more difficult, your static (static in that they're not infinitely healing, such as CH which for all intents and purposes we can kinda consider as such) heals don't get more effective. Therefore, a HoT which is healing 400 hp every tick for six ticks (Just an example) is no longer valuable in that your tank is going to get his ass kicked by something that (example again) is hitting for 600 hp every six ticks or so (variable, obviously, but I don't want to convert it to some dps that beats 400hp every 6 seconds. I'm lazy)
I'm not quite sure as to how one could balance HoT's to be more effective, except, say, effectively changing the way spells work so they're not tick based, but rather a specific set amount of seconds so that they can heal effectively for a much shorter duration, and perhaps even constantly. Once again, I'm not sure if this is even possible given the engine, but it'd be an interesting mix up for DoT's and HoT's in general (I think a tick based system is dumb)
This is all kinda rambling, but that's my take on the healing game situation, and perhaps someone who knows better than I do (most everyone, probably) will be able to figure out a solution given what was said.