JSS FAQ
upgrade to the latest jss, or, in the cryptomanager.initializationvalues object you pass to cryptomanager.initialize(), set removesunproivider=true.

JSS Provider Notes
if you do not wish the provider to be installed, create a cryptomanager.initializationvalues object, set its installjssprovider field to false, and pass the initializationvalues object to cryptomanager.initialize().

Mozilla-JSS JCA Provider notes
if you do not wish the provider to be installed, create a cryptomanager.initializationvalues object, set its installjssprovider field to false, and pass the initializationvalues object to cryptomanager.initialize().