Fixed : You cannot delete a plugin while it is active on the main site.
You will get this error in your site even though it was not an multi site website. It wont allow you to delete the plugin which is already deactivated. In this scenario please check wether you have installed the w3c cache plugin. If yes please deactivate the w3c cache plugin and then try to delete the plugin which you need to delete. Now the delete will work perfectly.
Once deleted successfully please reactivate the w3c cache plugin if you need caching in your site.