Yes, animals should be allowed to participate in the witness protection program. Pets are an important part of many families, and can in some cases serve as actual witnesses. Witnesses that own animals should be allowed to have their pets accompany them, within reason. They can serve as comfor in a very scary situation. In the case of an animal witness, these animals should also be protected as any other witness would be.
Yes, animals should be allowed in the witness protection program. Individuals who enter the witness protection program give up their entire lives to start over. They should at least be allowed to keep their pets who are often considered part of the family. Security measures would have to be taken to protect the pet's identity as well (new name, remove tracking chips, etc.) but it would be worth the effort.
Animals should not be allowed in the witness protection program. Animals should also not be allowed as evidence in a trial, unless the trial is about animal cruelty. Animals are not very viable witnesses to crimes. If the witness protection program is actually a rescuue program for neglected animals, then it should be renamed as such.
Sadly, I think families must leave behind their pets when they enter into the Witness Protection Program. First, I think the cost of putting even a single person in this program is probably very costly. I do not think that we should be spending that sort of money on an animal. I know people think that animals are a part of their family, but they are animals, not humans. Secondly, people entering into this program are expected to leave everything behind and change all their known characteristics. Common sense dictates that animals are part of what you would have to leave behind.