Perhaps have a dummy script that launches the tkinter script? The dummy script (the one directly launched from the toolbox will finish, but the tkinter one will continue (but be independent from the toolbox and act as a stand alone script without ArcToolbox functionality - i.e. won't add output layers to the TableOfContents, etc.).
Is it just annoying to have the toolbox dialog, or something else? Seems that it really is "appropriate" that the toolbox dialog is there because the script is still actually running until something is clicked in the tkinter GUI, right?