We've already got a plan in place to track overheals and blowthrough heals along with actual heals. It still won't be exact but it will be a lot more accurate than it is now. The basic approach will be to track incoming damage on each combatant and use that to track how much of a heal was actual heal, how much was a blowthrough (actual heal + extra heal that was needed) and how much is overheal (no actual heal, just overheal). Where it won't be exact is when a players max health changes due to buffs and such during an encounter, but it's the most accurate way we can think of at the moment.
Can't you look at the amount of threat that a heal generates in order to compute effective healing?