Exactly! That is thought provoking, interactive gameplay.
The answer to this question is the situation dictates which skill you would use in this case. For example, let's say my idea was implemented (PoM is now a full time buff given/refreshed through Benison); PoM is about to fall off, which means so is your DPS; but one or more players are below 50%. What skill are you going to use, especially knowing that if you don't use Benison, it's going to be 30s before you can get PoM back up. Also keep in mind that the PoM buff is also responsible for the increased lily generation.
The thing about that last situation is you were already not playing optimally that forced you into having to make that decision, because you're likely going to lose either your buff, or the player will KO as a result. You were too focused on nourishing the blood lily through Afflatus, and forgot to use a lily on Benison to refresh your PoM. BUT, the nice thing here is that it IS possible that the shield from Benison can provide just enough protection to the player to keep them alive, and also refresh your buff.
As a healer, it should always be more important to keep everyone on their feet, so in that situation if the player is too low you actually have no choice but to let PoM drop, and accept the DPS loss. That is your penalty, for focusing too much on damage in the first place. I absolutely love this aspect in such gameplay. The irony about this set up, is that not only will this more interactive kit potentially allow the WHM to cause damage in a way that adds thought and fun to your Glare spam, but it also maintains the vision the devs have for the job.
As for Benison not being available right away. I know it is a bit of a drawback, but one I know I would trade in a heartbeat to have more interaction with my job gauge and just passively gaining lilies to overheal with in order to use Misery.