Which wrapper are you walking about? The there are no additional jquery libraries included in your website without you adding them. While you are logged into the CMS, those are included because they are needed for the UI to function. Also some out of the box webparts are dependent on jquery and other libraries so they are automatically included when those webparts are used.
You're not gaining anything by using aspx over portal development mode. If you really want to have control of your markup, then I suggest using MVC. With both MVC and aspx development modes, you run the risk of coding yourself our of future upgrades because of all the unnecessary additional code you're adding.