Hi Jonas,
I haven't tested since I don't have any Python/TKinter environment, but try this.
In pure Tk there's a method called "wm" to manage the windows. There you can do something like "wm withdraw .mywindow" where '.mywindow' is a toplevel.
In TkInter you should be able to do something similar to:
root = Tkinter.Tk()
root.withdraw() # won't need this
Hope it helps