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First off, I thought this issue was kind of neat. It was very different, and that was one of the reasons I liked it. They didn't kill the badguy for a change. In fact they actually arrested the badguy. Also, the badguy wasn't a through and through evil villain. Dorjander was a Jedi who got sidetracked on a vendetta, and was quite ready to throw himself to the dark side. Zayne called his bluff and made use of that small shred of decency that Kace still has.
I admit, it was a risky move for the issue cause it was very anti-climatic. People like seeing death, violence, and action. It's all good drama. It provokes emotions. What John did was very non-traditional for Star Wars. But, for me, I thought it was very true to the characters.
As for the arc being a waste of time and nothing happened, you could say that. But then again, Zayne had an adventure (which is pretty much what the whole KOTOR series is about: adventures of Zayne), and furthermore Zayne changed a little. He's maturing more and gaining more wisdom. He's growing as a Jedi and as a person. Plus he's now committed himself to helping bring an end to the war, which is a very big step (and opens the door for more adventures).
It depends how you look at it. But I can definitely understand how people might be upset (dissatisfied) with how War went.