No contradiction if you follow the logic and the evidence.
"*** NOTE ***
Arneson contradicts himself and actually points to a 'wolf-like' creature (Pakicetus) supposedly evolving into a whale (cetacean/dolphin).
Carl Zimmer used the description of ‘wolf-like’ for Pakicetus in his book."
Any mention of Pakicetus as "wolf-like" is an analogy, and was meant to help the reader understand something of what it might have looked like. I didn't find that term applied to Pakicetus in my copy of "At the Water's Edge". You might want to provide a page citation for that claim. In fact, on page 203, the diagram showing the whale family tree has the following statement.
"A provisional phylogeny of whales. While there are many species not shown, this tree includes the major branches of whale evolution. A few caveats: some reconstructions (such as Pakicetus) are based on very limited fossils. Also, because the mesonychid relationships are so unclear, future research may show that whales actually have a more recent common ancetry with a particular mesonychid species. Finally, this tree is based on morphology: molecular studies don't agree on some of the branchings."
Zimmmer published "At the Water's Edge" in 2001. The post-cranial skeleton was unknown until its discovery by Thewissen in that year. A consensus has developed around an artiodactyl ancestry for whales. Mesonychids were proposed earlier because of a similarity in teeth. Other morphological features (such as the ankles) and DNA and biochemical analysis point to artiodactyls and not mesonychids.
Pakicetus was not related to wolves which are carnivores. Mesonychids and artiodactyls come from a completely different branch of mammals neither Zimmer or the scientists are proposing a wolf to whale evolutionary model.