Knives are no worse then any other weapon chain in my opinion. The potential for 3 dice of sneak attack sounds pretty powerful, but for 2/3 of them the character is rooted on the spot - have a mobile enemy, or one with reach, or doing ride by attacks and it seriously diminishes their damage output.
Supremacy has a "fail damage save" attack, as do many of the chains, no big drama there. Mastery has a multi-strike trick, but it's not that bad - knife damage is pretty low, and they only get sneak attack on their first attack - the big benefit is the DM has to roll 3 damage saves, so the potential for a low roll is greater (plus they have to hit by 10 for max effect - doesn't come up a lot in my experience, most get 1 or 2 hits).
As long as you remember that they have to make a move action to get into their stance (and can't simply "live in it"), and lose it if they are helpless, prone or sprawled, as well as not being able to move you won't have any real problems - just don't have the enemy walk up, and stand around while being flanked and shanked to death.