CKEditor break quotes: Why?
If deleting any function from a contributed module works for you without giving any issues, then it's totally ok except that the next module update will override your change and you will have to delete the offending lines again. So the best course is to report this to the contributed module's developers, so they fix and commit necessary changes.

By the way, this seems to have already been reported on https://www.drupal.org/project/ckeditor/issues/2957580.