I like weird, low fantasy settings, where magic is alien and dangerous. So I'm not a fan of the instantaneous, no-risk magic healing that's a staple to fantasy RPGs. I wrote about this before.
So, if I want magic to be inherently alien, and opposed to the natural order of things, the easiest way to go is treat a "benevolent" healing spell as you would a curse: the target of the spell must make a save or a resistance roll. There is no option to "let the spell take effect". If a character can shake off a curse or hex, then why should the reality-bending, flesh-mending healing be different?