^ I'm not sure about that. There might be a fair amount of crew on the ship who would object to a Borg chief engineer.
In any case, Janeway is making a decision that affects her ship and everyone on it: the question of who is chief engineer. And like I said, Janeway broke no laws in doing what she did; wouldn't you think somebody would have brought it up if she had no right to order B'Elanna to undergo the procedure?
As much as some might like to think otherwise, Starfleet is a military. (It's not militarISTIC, but it is still a military.) Those in the military don't have the luxury to not follow orders just because of morals; they can resign their commission if they can't handle it, but obviously B'Elanna couldn't do that here.