There is absolutely no reason for a car to break down because of jump starting if:
1- The cables were connected correctly. Cars use same voltage etc.
2- The battery is not broken (eg. cant accept charge anymore)
1 is obvious. The reason for 2, if battery cant absorb energy, removing jump leads can lead to a voltage spike and this is of course harmful. You would have same effect if you disconnect the battery of a car while engine is running.
So, it is safest to charge the empty battery and then restart the car on its own power. Because you can also see if your battery can hold charge (absorbing power) or not.
Here, you have to understand that the problem is not related to soft start charging, arcs etc. It is not even related to jump starting. Considering if you did everything else right. The only dangerous part left is removing the jump leads. Do a web search for "removing battery when car is running". If your battery is completely broken, you may have the same effect when removing jump leads. Because you are disconnecting the donor battery which may be the only working battery in system.
I found this thread to be interesting also :
Jump Start Destroying the Electronics - Myth?
I believe most often the damage is caused by people too tired or dumb enough to connect cables wrong way but not even realizing it even afterwards, then thinking that jump starting broke their car and then telling this story to others. I bet many do not even know that it is important to connect + to + and - to - . It takes only one person to tell that jump starting broke his car and the fear spreads like a disease.
I also think that in the past some people attempted jump starting 12V systems with 24V systems then decided jump starting is dangerous for electronics...
In addition, of course marketing departments are not helping either. They know that people are scared of jump starting cars because of electronics damage, wrong connections etc. So, they promote the fear even more so they can make sales on expensive cable sets. Honestly, probably the cables which can detect incorrectly made connections and refuse to work are probably useful in case you are color blind or in case if the user is expects that the cable will do everything for them automatically.
When all these information is passed from person to person, some of the facts are lost and usually one thing is left : 'jump starting broke the car'. Of course when the factors leading to result are lost, and you do not have understanding of how electric behaves, it is easy to believe in this myth.
Also some fun info, do not use defibryllator to jump start your car :
MythBusters - Defibrillator Jumpstart