Magento provide command line utility for it example
php bin/magento module:disable -f Magento_Wishlist
as Magento wishlist depend upon the other module as well so using without [-f] will not disable or enable the module and will display warning like
after using command with [-f] flag will solve this issue
please check the warning when you are using command forcefully
Alert: You used the –force option. As a result, modules might not function properly.
You may check complete information here as well http://devdocs.magento.com/guides/v2.0/install-gde/install/cli/install-cli-subcommands-enable.html#instgde-cli-subcommands-enable-modules