Thankfully my commission was commanded by Her Majesty and not a politician.
As I see leadership and command as two distinct elements (and trust that the promotion boards do actually ensure that at least a few candidates have both elements correctly intertwined) I am content with both sides of this. The man is 'free' to speak-out on such a major issue that directly impacts his men and that commanders are free to remove a subordinate's command status as they see fit. The system appears to work and work well for militaries that exist to support a democracy and its people.
Discipline does not equal blind obedience; subordinates get to evaluate the lawfulness and proportionality of all orders and judges can act as the ultimate arbitrators. Nobody said juggling the ever-conflicting requirements of orders, war-fighting, leadership and command was easy, especially when killing is involved. I've been in the dock twice to be judged by civilians over my military actions. It is scary to be under such scrutiny and the stress is immense (especially as the MoD abandons you, you know... just in case) but the court process is done with understanding and grace. Given what we do (or did for some of us) I have no difficulty with the post-Nuremberg position.