Everyone wants her to go full gamer and try and burn out the scavs from the setting but it isn't really herself that Motoko would be worried about in that scenario. It's Jun, Hiromi, Ichi, Malcom, Jackie, Vic, Misty, V and the rest that she's worried about.
You can't protect people in Night City. Not because of gangs or corporations but because of something that the average player might not think about. The real problem to protecting anything you care about in Night City is the fixers.
They pride themselves on using information as power and are far less protected then the average HVT in Night City, but they use that perceived weakness as a shield. They aren't too hard of a target to hit, but hitting them will most definitely result in being hit back. They go for the mutually assured destruction approach to protection.
The fixers of Night City would not have too much trouble finding Motoko, then her family, and then her friends, and you can bet that more then a few of them would be more then happy to sell her down the river in exchange for something as simple as a favor owed by the Bratva.
Put simply if you wanted to achieve as near a total safety net that you can get while living in Night City? You would have to speak the language of fixers, information. You would have to be able to blackmail or otherwise reach anyone at anytime and make sure they know that you can... If you can do that? You are officially the scariest person on the continent of North America, which comes with its own problems. : P
Still that would likely be the best path forward for her if she decides to pursue this. Incriminating photos in one hand and a Nekomata in the other.
Become the woman that everyone goes to and nobody crosses.
Become the urban legend that ends all other urban legends.
*Cough*...And now for something completely different.
Behold my tactical genius!
Jun: "Motoko what is that?"
*Jun points out the window to the balcony of a scav den where an unconscious scav is tied to a large purple balloon. Motoko watching on nearby laying upon a railing, while using a nail file to sand the blood off of her fingertips.*
Motoko: "That Jun is my latest piece of genius, I call it the Fulton recovery device!"
Jun: "Toko, you tied a large purple balloon to a man that must weigh over two hundred pounds."
*Another two purple balloons attached to the man start to slowly inflate.*
Motoko: "Ah, it's still hitching up during the inflating process. I'll need to work on that part so this goes faster."
Jun: "Motoko, why did you do this?"
Motoko: "It's in the name Jun! It's a recovery device. Meant to recover people or things that I can't carry with me back to my lai- home."
Jun: "Motoko how are you going to recover anything after sending it into the air on a balloon?"
Motoko: "That part is easy Jun, you just have someone swing by in an AV and grab the package with a wire."
Jun: "We don't have an AV."
Motoko: "We don't have an AV yet. It's on the list."
Jun: "The list of things we all swore never to let you have?"
Motoko: "The very one! But now that you have seen my tactical genius you will have no choice but to fold to the demands still listed in my Arasaka shopping cart!"
*The balloons finish inflating and the scav is quickly lifted away into the sky and carried away on the winds.*
Jun: "...The answer is still no."
Motoko: "...Fine the next test run of this is going to be on your refrigerator."