Hello Apollo,
There is a way to hide elements from the Structure View (one such method is offered by the free AXCM plug-in). What happens when you use AXCM (or other methods to hide elements) is that the elements get wrapped into hidden content. This might make the structure view less complex for your authors, but has a number of disadvantages and dangers.
1. The structure is normally invalidated, as the helper elements are usually required.
2. Accidentally deleting hidden content may make the invalidation permanent and render your documents useless.
It is NOT good practice to hide elements from authors in the structure view. Instead, you should either teach authors about the structure, or let them work in the Author View while adding sufficiently clear formatting to show them the underlying structure. In some cases, it might be better to create an authoring structure which is automatically transformed into the required full structure using an XSLT or other processing step. I have created a couple of such environments and they work fine. It just depends on the difference between the structure required for further processing and the structure that would be optimal for your authors (which in turn depends on the level at which your authors are experienced in working with structured content).
I hope this helps you solve your problem without having to tweak the structure view.
Kind regards
Jang