Simply put, I doubt the ninja world would allow Sasuke to become a rogue ninja again and far more people would be sent after him.
He’s already severely weakened since losing his rinnegan too btw
Surely Itachi knew how dangerous to the world the guy was, yet he only took his hand.
Also did Orochi not have his shed skin jutsi by then? That would have negated the lose of the hand...
I guess it should be assumed that it would have been costly for Itachi to kill Orochi.