Because Yorinobu is pretty much anti-corpo just like Johnny. Remember this is a guy who gave up his privileged life to join some anti-corpo rebel group. Despite coming later back into the fold he clearly never actually changed his mind about it. He just waited for the chance to destroy it from the inside instead. Because as Johnny already proved just blowing something up as an outsider does nothing.
Also I would say you are not really a victim of the Arasaka family machinations. Remember the Voodoo Boys wanted to contact Alt and wanted the Relic with Johnny in it for that so they hired Evelyn who in turn went to Dex who in turn went to V and Jackie. Besides the Relic being Arasaka tech they literally have nothing to do with what happened to you. That's why Saburo accepts it readily when you say that you want to repay your debt and put things right. None of the Arasakas actually have any bad blood with you. For them you are just a thief who fucked up by meddling with technology you shouldn't have and is looking for a fix.
The event of Yorinobu murdering Saburo and taking control would have happened even without you. Just were just a witness after all and not a cause.
That's why it makes sense why in all other ending you don't get involved with the Arasakas. They are not actually involved with you besides making all the tech.
Ok I must have missed all of that. I didn't know. Just assumed he was after the company he wanted to take from this dad. Still though, all that time with Johnny in your ear blasting Arasaka hate, I naturally looked upon them as the antagonists. Also as I said before when Johnny is in the tower, crashing right into the board room, it's natural to think "Here we go!"
Well the option to kick away the gun is on a timer. I kicked it naturally, but I wonder what might have happened if you just let the timer run out.
I think lots of people sleep on this "mechanic" and think they always need to choose if they might also not choose anything.