Yay for discussion!

Boo for the fact that you still like your card manipulation.

I had hoped to sway your opinion because it makes a faction of mine seem derivative. But assuming that there is merit in changing the ninja:
I agree that you don't want the ninja ability to be too over the top, but what I like about my suggestion is that it
feels more like you have ninjas at your command. Messing with Cards is nice and all, but my American-ized view of the ninja is that he's got swords and stealth and strikes out of no-where, causing panic! That's what I want them to feel like when I use them.
My attempt at not going over the top was that you don't get to use the ninja attack at any time or on anyone. You have to plan your attack many turns in advance. Plan well and it very well could be devastating. Plan poorly and it's a minor annoyance. It could have any number of one-off effects, from canceling the move orders to damage to courage checks, or some combination. I'm really not all that tied to exactly what the effect is. I liked Ajax's thought that you could buy more than one ninja strike, but maybe at escalating cost.
What I like about your alternative is that it simulates the leader getting picked off from a ninja attack. I guess when you start making combat rolls I don't think about army abilities, I think of units. Not that there's a problem with that - maybe you just get to buy units of ninjas.
I'm not completely convinced that you couldn't balance a ninja strike option in the Opponent M&C phase. Maybe something like "once per your opponent's M&C phase, reveal and discard a ninja strike card to make a (1)7/
6 attack on an unengaged enemy of your choice (your opponent may play command cards if they wish, but you may not). If that unit takes damage it must pass a courage check at C -2 or change it's standing order to hold and may not be changed this turn."
First of all, Attack Power 6 - come on man, they're ninjas!

I also think that you should give the enemy unit an out, first by allowing them to use defensive command cards and secondly to give them a chance at a courage check. The theory being that my Hawk Courage 16 Knights are highly motivated to continue their charge into the puny weaklings before them, even if their captain is killed. My scaredy cat Peasants, however, would get highly nervous if their leader got suddenly skewered by a ninja attack. Adding Ninja Strike as a card allows a couple of things - primarily the ability to play it in the opponent turn without tracking weird things inconsistent with BG in general. It also allows for some nifty ninja art! You could get one for free as the faction ability, and each additional one costs X points more.
The samurai cookie was just a quick thought if you wanted a more traditional, weaker ability for the army outside of the highly unusual ninja. And the top 10: I'm certainly open for whatever there, I just wanted to give you a response from an outside perspective. Ronin for Arquebusiers sounds perfectly reasonable.
I'd have to actually play with the Oni / Goryo. They do seem a bit out there, but the idea is cool. I admit I mostly got fixated on changing you off of card manipulation so I wasn't thinking about the rest as much.

I like the thought that they don't count for victory conditions - but I'd have to see how that works out for both sides.