Assuming reasonable suspicion, we have a case where our drug dog got distracted by defendant's pet dog inside the vehicle during a narcotics sniff and couldn't complete the sniff, while the defendant is temporarily detained. Animal control arrives and removes the pet dog to complete the sniff.

Defense say this intrusion isn't allowed because defendant wouldn't give consent to remove the dog. It seems like this should be okay as it's needed to complete the investigation and is reasonable under the circumstances, but I am not sure, and I'm also not sure my case law is on point. Has anyone dealt with something like this?

Well, in a traffic stop, you can detain all passengers of the car, so I guess you could argue that the dog is a passenger and could be properly removed in that way.