Most cars with programmable keys, need a key (original factory) to program other keys. If the original is lost and none are available it may be possible for the dealer to clear out the programmed keys and start from scratch, maybe not. However you do need a factory type key, they are not usually cheap. If you had a New computer put in and a factory key, it is programmable. If you just have a plain metal key it will not work, there needs to be the "chip" inside the plastic handle and there is a programming sequence to follow.
Damage using the wrong key? Well the anti theft system goes into lockout as you described, however it should unlock after a period of time, or the dealer could unlock it (there has to be a way). It sounds to me like you just have the wrong type key.
Yes, that is a different story. I really don't understand why nissan cannot tell them what to do? How did the first dealer have the key made when there was no key? A locksmith could take the lock cylinder apart and going by the tumblers, make one. If they used the lock cylinder from the ignition switch something may have not been put back properly. Also, was the car trying to be started with the wrong key with the new ecm?
Now that I have more info I might be able to help, but understand I do not work for nissan, and there is no way in heck they should not be able to figure it out how to make it run again.
So I take it that the new ecm was trying to be started with a factory key, there is a programming sequence that must be followed for this to work. The first dealer should have been able to make a factory key with the vin# XXXXX proof of ownership.
If something was disturbed (and they somehow used the ignition lock cylinder to have a new key made) that could be the cause. The only other cause I can think of is possibly the Bcm (body control module) which might hold the key code as well as the pcm are not in agreement. A lot of cars use the bcm and the pcm to verify the key. I do not have my manuals in front of me now, I am at home and trying my best to help.