Perhaps the drone had small self-destruct mechanisms for most secret pieces. But it clearly had no self-destruct for the entire airplane, for whatever reason. I can think of safety of maintenance and operation as one such reason; it becoming a bomb as another reason. It's one thing to fly an unarmed drone over Iran, and a somewhat different thing to fly a drone with explosives. Casus Belli and all that...
Or we can not program a cruise missle to find and destroy this before they can reverse engineer it?
Cruise missiles are not hounds. They don't fly around and find things. They need to be told in no uncertain terms where to go and what to hit. In this case nobody knows where the drone is stored. Perhaps by now it's even hard to tell because one wing is in Bejing, another is in Moscow, and the rest is being carefully taken apart, with seven video cameras taping everything, on lower floors of one of Iranian subterranean nuclear installations that can't be taken out with a megaton nuke.
I realize we are quite as adept as Hollywood reality but surely we have better contingency plans than this?
As for cruise missle, I realize they need programed and have vivid mapping to follow terrain, but we know where they will reverse engineer this thing, time to take it out as we follow it to its location, our spy satellites can certain provide that information.
I read on a military channel they think it ran out of fuel!