Ehh, I don't think it's that big of a problem. There shouldn't just be a get rid of Condition check each one should be a different roll at a different difficulty. Getting rid of someones Fatigue shouldn't be as hard as getting rid of a Stun for instance.

If it bothers you so much, don't let the obviously magic conditions like Polymorph be on the list of conditions that can be Healed away.