Using paragraphs tag instead of div in fields?
The extra junk is added by the field.tpl.php file from core. 
But hey you can customize it.

Create a new file in your theme's templates folder. (For available variables, see here)

File name: field--body.tpl.php  (See http://drupal.org/node/1089656 for template file suggestions)
Contents:


    


Now, when you use render() in your node.tpl.php files, you will see the p tag wrapped content instead of the extra junk.

Update: I have forgotten that the $item comes from $items array. Updated the code above. If the body field has multiple instances, each one will be shown in individual p tags.