The recovery system we have for ability/level drain/damage might not be perfect, but as Zelk said too, the basics work. In practice, mostly this means
1) Logging in for the next session after a few days since the last means your PC has had time to recover and will be ready for adventure again.
2) You can't shrug the damage off with a 1st level heal and keep on pressing whack-a-mole.
3) Ability damage as-is is cleared by Lesser Restoration, which is too trivial to get to scale back whack-a-moling in most instances.
As for availability of Restoration, SRD-wise a party without a cleric would go to a temple in a town for it. We do/could/should have recovery spells as services, no? DMd it can of course be done, but I thought even some scripted ones exist. The whole point of a floored penalty is that you'd feel consequences that can't be shrugged off with a lvl1 or 2 spell on the spot and keep on whack-a-moling.
The main point is that DMs could have a tool to send PCs falling back with tails between their legs without outright killing them. You seem to turn it on its head Ithildur, and assume that PCs are then supposed and required to carry that fantastic on-the-spot-fixall magic to survive. That would simply be bad DMing. The deal changes the battle landscape towards more nuanced than grinding waves of near-TPK encounters whack-a-mole, and of course the DMs, Viigas included, will adapt. And it's not like a DM couldn't give a party a wand of Restoration if some higher-levels are sent to an epic battle of attrition. (Anyone with a single level of a non-ranger divine caster can use that, unless the ACR stripped Restoration from nwn2 druid spell list?) But that should be the exception. Usually PCs should feel the attrition of repeated near-death experiences.
It's one of those awesomely-harmonious changes where an overpowered class loses power and feels more useful.
A good point, especially in "overpowered" meaning a mighty engine of personally-delivered desctruction, as opposed to party support. But it doesn't change that "more useful" still does carry the risk of twisting the playerbase towards more and more divine casters, and can make a divine caster feel indispensable for a higher-level party. (How indispensable it really is, of course depends on how the DM designs the sessions, how much attrition is present.)
On the other hand, a custom flooring penalty that can't be healed by magic, but only by time, does seem to go counter to the spirit of DnD in the sense that fantastic magic is fantastic. To every affliction there is a fix at appropriate fantasticness level. (And the magic increases DM flexibility for the cases when an epic battle against attrition is desired.)