Apollo,
While, as has been discussed already, you cannot hide elements in the Structure View when they are shown in the document window, you can collapse them so that substructure that is generated by XSLT is not shown.
You might also consider naming conventions that distinguish such automatically created elements from user-created elements. For example, if the XSLT-generated elements all have names that start with ZInternalUseOnly, users should understand that they should avoid manually manipulating them. The initial 'Z' will move the names of these elements to the bottom of an alphabetical list (such as in the Element Catalog window).
--Lynne