@DeAnno: The difference, of course, being that humans can actually consider such possibilities and could communicate our preferences on them. Dogs have no ability to do any such thing. Besides which, I personally question your assertion: while *I* have no desire to cease, I also am quite unattached to being human; I would cheerfully exchange my humanity for a more intelligent alternative. Obviously, the dogs aren't being given options such as "upload into the robots" or "mod your brain to human cognitive ability" but then, they wouldn't know what to do with such options if offered. Not all steps in cognitive ability are equal. Also, don't forge the point mentioned near the end of the story: a suffering human (usually) has the agency to end emself; a suffering dog usually does not.
Regarding genocide, while it is a useful heuristic to say "X is genocide => X is bad", that doesn't make it universally true. Genocide (when discussing species, not "races" of humanity) is simply the end of a genetic line; the negative utility of genocide depends on the positive utility of that line (both directly, and considering externalities such as the value it contributes through enriching diversity in the ecosystem). We consider dogs to be of pretty high utility (they're comforting, cute, useful workers both assisting humans directly and performing tasks such as killing rats, and edible), but we consider smallpox to be of quite negative utility. As for suffering, bear in mind that the story implies that the Extinction was a matter of targeting the reproductive systems; the surviving animals would have presumably lived out their lives as happily as they would have been anyhow, but they wouldn't have had children (and bear in mind that we routinely neuter pets and livestock today).
I have no clear feelings on this one either way, but nobody here seemed to be arguing in favor of the protagonists' viewpoint.