Saying Mi Sheberach for Tzahal is in no way an endorsement of the medinah. That said, it is our Torah study and Emuna in Eretz Yisrael which keeps us (and the secular yidden by default) safe.
Also, the Gedolim disagreed with the secular medinah, but they all agree that one should live in Eretz Yisrael regardless. Too many people in this thread are using the state as an excuse for their own short-falls.