After further research that was a pretty bad solution, that class is used to decorate other classes so who knows what gets broken by doing that. I found a better easier solution that solves the html rendering and the subpages:
In the cms/code/LeftAndMain.php on line number 388 you'll find a $sitetree variable being set, change that to this:
This is a better solution because your not messing with the core code and should only affect the Sitetree. All the decorator Hierarchy class does a simple php eval on the template so the inline ifs should solve the issue. The tree looks a bit messed up, but everything works I'm sure you guys can figure out a way to hack the css to fix the tree. Also the code is a bit messy I was trying several different things so you might want the extraneous inline ifs deleted.