I'll look at the jQuery ordering in the header.  In most cases you don't need to load jQuery plugins in the header.  They will work just fine if you inject them in the page before their first use.

I am not sure what you are refering to about "turning it off" in the host settings since jQuery does not provide a method to turn it on or off.  The injection of jQuery in the page is controlled by individual modules or framework features.  The host settings only allows you to determine where to load jQuery from - either local or hosted.  Most likely jQuery is getting loaded on your site because you have the Widget framework enabled which requires jQuery.