The manpage says that directly invoking a script from package.json with `npm run X` aka `npm run-script X` will still work with this preference set to true, but that it will not run pre/post scripts. Perhaps that is good enough for your use-case?

  npm help run-script
  
   [...]
   ignore-scripts
       o Default: false
       o Type: Boolean
       If true, npm does not run scripts specified in package.json files.

       Note  that  commands  explicitly  intended to run a particular script, such as npm
       start, npm stop, npm restart, npm test, and npm run-script will  still  run  their
       intended  script  if  ignore-scripts  is  set,  but  they will not run any pre- or
       post-scripts.