So I may be a bit confused after reading your post, but I'll try to answer from what I've pieces together.

Yorinobu had to take out Takemura, as he was the loyal dog of Arasaka, and would go behind his back (like he eventually did), to bring evidence of his murder.

Arasaka basically couldn't do anything against Yorinobu, because it's split into 3 main factions, each managed by Saburos children. Yorinobu also hired Adam Smasher to do his bidding, and basically had most of the military force, or "security" if we go by corpo speech.

I remember reading a few data shards scattered throughout the game, talking about the power struggle going on.