Try purifying the Yokai realm pools with ki pulses - this will put your ki recovery back to normal for a short time - AND it gives you anima for yokai skills.
Barrier talisman and sacred water are also pretty great - both increase ki recovery; use them when they inflict dark realm and you won't have much issue.
Of course, barrier has the added benefit of purifying pools for you - meaning you can have ki recovery I'm the dark realm that is even better than your ki recovery outside of it.
Seems like pretty good game design to me. It's meant to force you to use more yokai skills and plan your attacks more carefully, but you are given the tools to be able to overcome it without doing that.
Seriously - work on purifying and if that isn't enough, get some sacred water (you can buy it in the kodama bazaar) or barrier talisman.
The definition of insanity is doing the same thing again and again, while expecting different results. (As defined by Einstein) Maybe we're all a little crazy.