This.
There's exactly one problem that seems to be the reason to swing the nerfbat at Divine Casters and its not Lesser Restoration, it's Turn Undead. Otherwise you'd also have to ban Bards and Druids. Lesser Restoration and Lay on Hand not curing Worms is a simple matter, there's no Rulebook reference about a worm plague turning people into undead being dead set to be a run of the mill disease.
From an onlooker's viewpoint your're more or less attempting to use dynamite to remove a couple daisies from your flowerbed. Rather than just getting rid of them manually and going ahead with your campaign.
There's a mere 2 minor fixes.
1. Turn Undead doesn't seem to work in the region or on the Worm Undead in particular.
2. It's not a nasty cough, it's a magical plague and Lesser Restoration isn't gonna cut it. Might as well not removeable by anything shy of Greater Restoration or specifically brewed potions you're in charge of distribting in amounts that makes sense for you.
I'd personally take Lycantrophy as reference for a magical disease with an physical component. Lesser Restoration is simply not gonna cut it and your players aren't ever gonna second guess it.