This.

Mana Pool for ret and prot doesn't change with gear. I have the exact same ticks from Divine Plea as ret and prot, but the tick is 3 times as big in holy gear.

There are only two ways to modify this spell, since it only has two effects.

Effect 1: Mana Regen
Effect 2: Healing penalty

If the ability is too powerful, you can either nerf the mana regen or increase the healing penalty. Holy pallies will still use it at every cooldown unless they are in a world of hurt if the healing penalty is increased, so the only way to make it a decision is to nerf the mana regen. Make the holy pally say "Wow, is it really worth a healing penalty to get back 1500 Mana?" Even then it won't work in PvE unless the incoming damage is just brutal since the pally isn't the only healer. He can just say "I'm popping plea, back me up" and the other healers push a little harder. The only way to accomplish what this spell was INTENDED to be (which is a bloodrage effect for prot and ret) is to make a mandatory holy talent nerf the ability to the ground. If you take Beacon of Light, Divine Plea has a 75% penalty. Holy Pallies will still take it, but they will actually be drainable in PvP, which is where the real problem lies.

The final option is to add a 3rd effect to the spell that is meaningless to ret and prot and doesn't effect healing throughput. Have it reduce your crit chance to zero for the duration or something, so IoL can't proc. Someone creative could come up with something here, but as it stands, unfortunately, you can't make this spell a decision without making it worthless.