At this point, there is no workaround.
With SEP11, our system tray ran with admin rights, with SEP12, it runs with minimal user rights and lower integrity level requirements.
At the moment, our GUI is either all or nothing, and there are a number of items with the GUI that do need admin rights, so we have to elevate on opening, rather than for each specific item where required.
In the future, we would look to move UAC inside the GUI so that each item that requires elevation will prompt, but thats a massive change in the way our client is engineered.