We've never had both the damage and healing aspects of Assize work together. It's always been used for damage first, and if it lined up so that the healing comes in useful, happy coincidence, in HW Cleric Stance forced the choice between damage or healing, you only got one of the two. We also use Earthly Star in the same way, on CD for the damage, and if it lines up to heal, that's just a bonus. Having a second charge is the absolute simplest solution to the problem. If you want/need to hold a charge for healing purposes (cough UCOB), you can hold a charge. If you know you won't need a charge for healing, either due to optimization or just knowing the way the fight plays out, you can dump one whenever you cap, and spend both in the 2min window for more damage, as we do now with Phlegma. In fact, adding this small thing is at least 'some' extra complexity the class still lacks, so it'd benefit from that too.
Also, having 2 charges would actually improve versatility of 'when to use it as a healing tool'. Say you're doing, idk, P8S. The damage of Fourfold Fires (the vent proximity aoes) hits during the raidbuff window. Let's imagine Assize is up at the first oGCD possible during the buff window, for the simplicity of the example. Holding Assize to heal that damage would take like 7 seconds, wouldn't drop out of raidbuffs but it'd potentially cost a use off the end of the fight. However, going into the same example with 2 charges (or one, with ~5sec left for the next to come back), you could throw one out to get the CD going again as you would in raidbuffs, and then hold the second charge towards the end of the buff window, to heal the Fourfold damage, without losing a use because the first charge's use set the CD ticking again.
You're right that there's multiple ways to fix this, but having the 'damage half' turn into 'the healing half' is a recipe for disaster I think. If it was such a horrible idea for DRGs and their High Jump/Mirage Dive losing an eye to the Thordan transition in DSR, that SE reverted the change in the very next patch, then 'oops sorry I thought I'd be able to get the healing half of Assize in time' would be the bane of PF circus-show runs and optimized logging runs alike.