Yes, this book sends a different message. But let us not forget that Vimes now has a son, and that Stratford was going to attack that son. Pay careful attention to what Willikens says: that Vimes would have taken him (Stratford) prisoner, rather than kill him, even tho doing so would have torn him apart inside.
Now, consider Vimes options. He can either punish Willikens, or reward him, or let the matter lie.
Consider also that Stinky, and to a lesser extent, I think, Willikens are being guided by The Summoning Dark. Admittedly, I may be reading a bit into the book as it stands to come to that conclusion.
I think you're illustrating my point. Willikens kills (rather than captures) Stratford because he simply felt that Stratford deserved to die rather than face justice. What Stratford would have done to young Sam is irrelevant and Vimes' theoretical reactions to such an event are irrelevant; Stratford never succeeded. Throughout the book, Vimes tells others that Willikens is not bound by the same adherence to the Law that Vimes is. It's almost as if Vimes is giving Willikens permission to be a vigilante. It's quite likely that Vimes had an inkling that Stratford would attempt to escape. It's also likely that Vimes was aware that Willikens was following the coach. But do we have ever have evidence that Vimes tells Willikens that he should not kill Stratford if the murderer escapes? No. I think Vimes tacitly approves of Willikens serving as the vigilante, the one who can do all the nasty, barely legal things that Vimes himself should not do.
Also, Willikens is not affected by the Summoning Dark. He doesn't need to be, since he isn't subject to the same moral and legal codes that Vimes is. In a sense, he is Vimes's Id, the Beast personified. He doesn't need the Summoning Dark to convince him to murder because he is not subject to the same level as self control that Vimes must be.
I also don't think that Stinky is affected by the "violent" side of the SD either. Its influence on the goblins is more about understanding the darkness, rather than releasing its destructive potential, otherwise the goblins would have all fought back.